Slamseq iBet spikeIn Max P paper

In [43]:
from __future__ import print_function
import os.path
import pandas as pd
import sys
sys.path.insert(0, '../../')
import seaborn as sns
import numpy as np

from JKBio.Helper import *
from JKBio.helper import pyDESeq2

from bokeh.plotting import *
from bokeh.models import HoverTool
import matplotlib.pyplot as plt

from sklearn.neighbors import KNeighborsClassifier
from sklearn.manifold import MDS, TSNE
from sklearn.decomposition import PCA
from sklearn.preprocessing import scale
#from umap import UMAP

output_notebook()
%load_ext autoreload
%matplotlib inline
%autoreload 2
%load_ext rpy2.ipython
Loading BokehJS ...
The autoreload extension is already loaded. To reload it, use:
  %reload_ext autoreload
The rpy2.ipython extension is already loaded. To reload it, use:
  %reload_ext rpy2.ipython

downloading their data

downloading the data

In [2]:
version="v2"
project="slamseqMax"
location= '../data/'+project+"/"
In [4]:
mkdir ../$location
In [30]:
!gsutil ls gs://transfer-amlproject/200827_MP8179_fastq/
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_10_MP8179_S169_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_10_MP8179_S169_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_10_MP8179_S169_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_10_MP8179_S169_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_11_MP8179_S170_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_11_MP8179_S170_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_11_MP8179_S170_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_11_MP8179_S170_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_12_MP8179_S171_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_12_MP8179_S171_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_12_MP8179_S171_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_12_MP8179_S171_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_13_MP8179_S172_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_13_MP8179_S172_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_13_MP8179_S172_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_13_MP8179_S172_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_14_MP8179_S173_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_14_MP8179_S173_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_14_MP8179_S173_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_14_MP8179_S173_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_15_MP8179_S174_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_15_MP8179_S174_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_15_MP8179_S174_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_15_MP8179_S174_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_16_MP8179_S175_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_16_MP8179_S175_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_16_MP8179_S175_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_16_MP8179_S175_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_17_MP8179_S176_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_17_MP8179_S176_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_17_MP8179_S176_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_17_MP8179_S176_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_18_MP8179_S177_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_18_MP8179_S177_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_18_MP8179_S177_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_18_MP8179_S177_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_19_MP8179_S178_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_19_MP8179_S178_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_19_MP8179_S178_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_19_MP8179_S178_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_1_MP8179_S160_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_1_MP8179_S160_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_1_MP8179_S160_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_1_MP8179_S160_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_20_MP8179_S179_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_20_MP8179_S179_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_20_MP8179_S179_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_20_MP8179_S179_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_21_MP8179_S180_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_21_MP8179_S180_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_21_MP8179_S180_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_21_MP8179_S180_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_23_MP8179_S181_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_23_MP8179_S181_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_23_MP8179_S181_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_23_MP8179_S181_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_24_MP8179_S182_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_24_MP8179_S182_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_24_MP8179_S182_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_24_MP8179_S182_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_2_MP8179_S161_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_2_MP8179_S161_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_2_MP8179_S161_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_2_MP8179_S161_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_3_MP8179_S162_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_3_MP8179_S162_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_3_MP8179_S162_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_3_MP8179_S162_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_4_MP8179_S163_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_4_MP8179_S163_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_4_MP8179_S163_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_4_MP8179_S163_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_5_MP8179_S164_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_5_MP8179_S164_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_5_MP8179_S164_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_5_MP8179_S164_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_6_MP8179_S165_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_6_MP8179_S165_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_6_MP8179_S165_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_6_MP8179_S165_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_7_MP8179_S166_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_7_MP8179_S166_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_7_MP8179_S166_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_7_MP8179_S166_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_8_MP8179_S167_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_8_MP8179_S167_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_8_MP8179_S167_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_8_MP8179_S167_R2_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_9_MP8179_S168_R1_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_9_MP8179_S168_R1_001_fastqc.zip
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_9_MP8179_S168_R2_001_fastqc.html
gs://transfer-amlproject/200827_MP8179_fastq/Reports/20200827_9_MP8179_S168_R2_001_fastqc.zip
In [24]:
! gsutil -m cp gs://transfer-amlproject/slamseq_inhibitor_spikeins/*MP8179*.fastq.gz ../../data/$project/fastqs/
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_10_MP8179_S169_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_10_MP8179_S169_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_11_MP8179_S170_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_11_MP8179_S170_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_12_MP8179_S171_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_12_MP8179_S171_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_13_MP8179_S172_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_13_MP8179_S172_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_14_MP8179_S173_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_14_MP8179_S173_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_15_MP8179_S174_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_15_MP8179_S174_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_16_MP8179_S175_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_16_MP8179_S175_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_17_MP8179_S176_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_17_MP8179_S176_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_18_MP8179_S177_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_18_MP8179_S177_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_19_MP8179_S178_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_19_MP8179_S178_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_1_MP8179_S160_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_1_MP8179_S160_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_20_MP8179_S179_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_20_MP8179_S179_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_21_MP8179_S180_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_21_MP8179_S180_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_23_MP8179_S181_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_23_MP8179_S181_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_24_MP8179_S182_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_24_MP8179_S182_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_2_MP8179_S161_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_2_MP8179_S161_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_3_MP8179_S162_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_4_MP8179_S163_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_3_MP8179_S162_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_4_MP8179_S163_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_5_MP8179_S164_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_6_MP8179_S165_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_5_MP8179_S164_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_6_MP8179_S165_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_7_MP8179_S166_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_7_MP8179_S166_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_8_MP8179_S167_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_8_MP8179_S167_R2_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_9_MP8179_S168_R1_001.fastq.gz...
Copying gs://transfer-amlproject/slamseq_inhibitor_spikeins/20200827_9_MP8179_S168_R2_001.fastq.gz...
Resuming download for ../../data/slamseqMax/fastqs/20200827_4_MP8179_S163_R2_001.fastq.gz component 0
Resuming download for ../../data/slamseqMax/fastqs/20200827_4_MP8179_S163_R2_001.fastq.gz component 1
Resuming download for ../../data/slamseqMax/fastqs/20200827_4_MP8179_S163_R2_001.fastq.gz component 2
Resuming download for ../../data/slamseqMax/fastqs/20200827_4_MP8179_S163_R2_001.fastq.gz component 3
Resuming download for ../../data/slamseqMax/fastqs/20200827_2_MP8179_S161_R1_001.fastq.gz component 0
Resuming download for ../../data/slamseqMax/fastqs/20200827_2_MP8179_S161_R1_001.fastq.gz component 1
Resuming download for ../../data/slamseqMax/fastqs/20200827_2_MP8179_S161_R1_001.fastq.gz component 2
Resuming download for ../../data/slamseqMax/fastqs/20200827_4_MP8179_S163_R1_001.fastq.gz component 0
Resuming download for ../../data/slamseqMax/fastqs/20200827_4_MP8179_S163_R1_001.fastq.gz component 2
Resuming download for ../../data/slamseqMax/fastqs/20200827_4_MP8179_S163_R1_001.fastq.gz component 1
Resuming download for ../../data/slamseqMax/fastqs/20200827_3_MP8179_S162_R1_001.fastq.gz component 0
Resuming download for ../../data/slamseqMax/fastqs/20200827_3_MP8179_S162_R1_001.fastq.gz component 1
Resuming download for ../../data/slamseqMax/fastqs/20200827_3_MP8179_S162_R1_001.fastq.gz component 2
Resuming download for ../../data/slamseqMax/fastqs/20200827_3_MP8179_S162_R2_001.fastq.gz component 0
Resuming download for ../../data/slamseqMax/fastqs/20200827_3_MP8179_S162_R2_001.fastq.gz component 1
Resuming download for ../../data/slamseqMax/fastqs/20200827_3_MP8179_S162_R2_001.fastq.gz component 2
Resuming download for ../../data/slamseqMax/fastqs/20200827_2_MP8179_S161_R1_001.fastq.gz component 3
Resuming download for ../../data/slamseqMax/fastqs/20200827_4_MP8179_S163_R1_001.fastq.gz component 3
Resuming download for ../../data/slamseqMax/fastqs/20200827_3_MP8179_S162_R1_001.fastq.gz component 3
Resuming download for ../../data/slamseqMax/fastqs/20200827_3_MP8179_S162_R2_001.fastq.gz component 3
- [46/46 files][165.1 GiB/165.1 GiB] 100% Done 177.8 MiB/s ETA 00:00:00         
Operation completed over 46 objects/165.1 GiB.                                   
In [21]:
ls ../../data/$project/fastqs
mr193-MV411-MYBi_30m-r1_R1_001.fastq.gz_trimming_report.txt
mr193-MV411-MYBi_30m-r1_R1_001_unpaired_1.fq.gz
mr193-MV411-MYBi_30m-r1_R1_001_val_1.fq.gz
mr193-MV411-MYBi_30m-r1_R2_001.fastq.gz_trimming_report.txt
mr193-MV411-MYBi_30m-r1_R2_001_unpaired_2.fq.gz
mr193-MV411-MYBi_30m-r1_R2_001_val_2.fq.gz
mr194-MV411-MYBi_30m-r2_R1_001.fastq.gz_trimming_report.txt
mr194-MV411-MYBi_30m-r2_R1_001_unpaired_1.fq.gz
mr194-MV411-MYBi_30m-r2_R1_001_val_1.fq.gz
mr194-MV411-MYBi_30m-r2_R2_001.fastq.gz_trimming_report.txt
mr194-MV411-MYBi_30m-r2_R2_001_unpaired_2.fq.gz
mr194-MV411-MYBi_30m-r2_R2_001_val_2.fq.gz
mr195-MV411-MYBi_30m-r3_R1_001.fastq.gz_trimming_report.txt
mr195-MV411-MYBi_30m-r3_R1_001_unpaired_1.fq.gz
mr195-MV411-MYBi_30m-r3_R1_001_val_1.fq.gz
mr195-MV411-MYBi_30m-r3_R2_001.fastq.gz_trimming_report.txt
mr195-MV411-MYBi_30m-r3_R2_001_unpaired_2.fq.gz
mr195-MV411-MYBi_30m-r3_R2_001_val_2.fq.gz
mr196-MV411-MYBi_30m-r4_R1_001.fastq.gz_trimming_report.txt
mr196-MV411-MYBi_30m-r4_R1_001_unpaired_1.fq.gz
mr196-MV411-MYBi_30m-r4_R1_001_val_1.fq.gz
mr196-MV411-MYBi_30m-r4_R2_001.fastq.gz_trimming_report.txt
mr196-MV411-MYBi_30m-r4_R2_001_unpaired_2.fq.gz
mr196-MV411-MYBi_30m-r4_R2_001_val_2.fq.gz
mr197-MV411-PBS_30m-r1_R1_001.fastq.gz_trimming_report.txt
mr197-MV411-PBS_30m-r1_R1_001_unpaired_1.fq.gz
mr197-MV411-PBS_30m-r1_R1_001_val_1.fq.gz
mr197-MV411-PBS_30m-r1_R2_001.fastq.gz_trimming_report.txt
mr197-MV411-PBS_30m-r1_R2_001_unpaired_2.fq.gz
mr197-MV411-PBS_30m-r1_R2_001_val_2.fq.gz
mr198-MV411-PBS_30m-r2_R1_001.fastq.gz_trimming_report.txt
mr198-MV411-PBS_30m-r2_R1_001_unpaired_1.fq.gz
mr198-MV411-PBS_30m-r2_R1_001_val_1.fq.gz
mr198-MV411-PBS_30m-r2_R2_001.fastq.gz_trimming_report.txt
mr198-MV411-PBS_30m-r2_R2_001_unpaired_2.fq.gz
mr198-MV411-PBS_30m-r2_R2_001_val_2.fq.gz
mr199-MV411-PBS_30m-r3_R1_001.fastq.gz_trimming_report.txt
mr199-MV411-PBS_30m-r3_R1_001_unpaired_1.fq.gz
mr199-MV411-PBS_30m-r3_R1_001_val_1.fq.gz
mr199-MV411-PBS_30m-r3_R2_001.fastq.gz_trimming_report.txt
mr199-MV411-PBS_30m-r3_R2_001_unpaired_2.fq.gz
mr199-MV411-PBS_30m-r3_R2_001_val_2.fq.gz
mr200-MV411-PBS_30m-r4_R1_001.fastq.gz_trimming_report.txt
mr200-MV411-PBS_30m-r4_R1_001_unpaired_1.fq.gz
mr200-MV411-PBS_30m-r4_R1_001_val_1.fq.gz
mr200-MV411-PBS_30m-r4_R2_001.fastq.gz_trimming_report.txt
mr200-MV411-PBS_30m-r4_R2_001_unpaired_2.fq.gz
mr200-MV411-PBS_30m-r4_R2_001_val_2.fq.gz
mr201-MV411-MYBi_6h-r1_R1_001.fastq.gz_trimming_report.txt
mr201-MV411-MYBi_6h-r1_R1_001_unpaired_1.fq.gz
mr201-MV411-MYBi_6h-r1_R1_001_val_1.fq.gz
mr201-MV411-MYBi_6h-r1_R2_001.fastq.gz_trimming_report.txt
mr201-MV411-MYBi_6h-r1_R2_001_unpaired_2.fq.gz
mr201-MV411-MYBi_6h-r1_R2_001_val_2.fq.gz
mr202-MV411-MYBi_6h-r2_R1_001.fastq.gz_trimming_report.txt
mr202-MV411-MYBi_6h-r2_R1_001_unpaired_1.fq.gz
mr202-MV411-MYBi_6h-r2_R1_001_val_1.fq.gz
mr202-MV411-MYBi_6h-r2_R2_001.fastq.gz_trimming_report.txt
mr202-MV411-MYBi_6h-r2_R2_001_unpaired_2.fq.gz
mr202-MV411-MYBi_6h-r2_R2_001_val_2.fq.gz
mr203-MV411-MYBi_6h-r3_R1_001.fastq.gz_trimming_report.txt
mr203-MV411-MYBi_6h-r3_R1_001_unpaired_1.fq.gz
mr203-MV411-MYBi_6h-r3_R1_001_val_1.fq.gz
mr203-MV411-MYBi_6h-r3_R2_001.fastq.gz_trimming_report.txt
mr203-MV411-MYBi_6h-r3_R2_001_unpaired_2.fq.gz
mr203-MV411-MYBi_6h-r3_R2_001_val_2.fq.gz
mr204-MV411-MYBi_6h-r4_R1_001.fastq.gz_trimming_report.txt
mr204-MV411-MYBi_6h-r4_R1_001_unpaired_1.fq.gz
mr204-MV411-MYBi_6h-r4_R1_001_val_1.fq.gz
mr204-MV411-MYBi_6h-r4_R2_001.fastq.gz_trimming_report.txt
mr204-MV411-MYBi_6h-r4_R2_001_unpaired_2.fq.gz
mr204-MV411-MYBi_6h-r4_R2_001_val_2.fq.gz
mr205-MV411-PBS_6h-r1_R1_001.fastq.gz_trimming_report.txt
mr205-MV411-PBS_6h-r1_R1_001_unpaired_1.fq.gz
mr205-MV411-PBS_6h-r1_R1_001_val_1.fq.gz
mr205-MV411-PBS_6h-r1_R2_001.fastq.gz_trimming_report.txt
mr205-MV411-PBS_6h-r1_R2_001_unpaired_2.fq.gz
mr205-MV411-PBS_6h-r1_R2_001_val_2.fq.gz
mr206-MV411-PBS_6h-r2_R1_001.fastq.gz_trimming_report.txt
mr206-MV411-PBS_6h-r2_R1_001_unpaired_1.fq.gz
mr206-MV411-PBS_6h-r2_R1_001_val_1.fq.gz
mr206-MV411-PBS_6h-r2_R2_001.fastq.gz_trimming_report.txt
mr206-MV411-PBS_6h-r2_R2_001_unpaired_2.fq.gz
mr206-MV411-PBS_6h-r2_R2_001_val_2.fq.gz
mr207-MV411-PBS_6h-r3_R1_001.fastq.gz_trimming_report.txt
mr207-MV411-PBS_6h-r3_R1_001_unpaired_1.fq.gz
mr207-MV411-PBS_6h-r3_R1_001_val_1.fq.gz
mr207-MV411-PBS_6h-r3_R2_001.fastq.gz_trimming_report.txt
mr207-MV411-PBS_6h-r3_R2_001_unpaired_2.fq.gz
mr207-MV411-PBS_6h-r3_R2_001_val_2.fq.gz
mr208-MV411-MS2-r1_R1_001.fastq.gz_trimming_report.txt
mr208-MV411-MS2-r1_R1_001_unpaired_1.fq.gz
mr208-MV411-MS2-r1_R1_001_val_1.fq.gz
mr208-MV411-MS2-r1_R2_001.fastq.gz_trimming_report.txt
mr208-MV411-MS2-r1_R2_001_unpaired_2.fq.gz
mr208-MV411-MS2-r1_R2_001_val_2.fq.gz
mr209-MV411-MS2-r2_R1_001.fastq.gz_trimming_report.txt
mr209-MV411-MS2-r2_R1_001_unpaired_1.fq.gz
mr209-MV411-MS2-r2_R1_001_val_1.fq.gz
mr209-MV411-MS2-r2_R2_001.fastq.gz_trimming_report.txt
mr209-MV411-MS2-r2_R2_001_unpaired_2.fq.gz
mr209-MV411-MS2-r2_R2_001_val_2.fq.gz
mr210-MV411-MS2-r3_R1_001.fastq.gz_trimming_report.txt
mr210-MV411-MS2-r3_R1_001_unpaired_1.fq.gz
mr210-MV411-MS2-r3_R1_001_val_1.fq.gz
mr210-MV411-MS2-r3_R2_001.fastq.gz_trimming_report.txt
mr210-MV411-MS2-r3_R2_001_unpaired_2.fq.gz
mr210-MV411-MS2-r3_R2_001_val_2.fq.gz
mr211-MV411-JQ1-r1_R1_001.fastq.gz_trimming_report.txt
mr211-MV411-JQ1-r1_R1_001_unpaired_1.fq.gz
mr211-MV411-JQ1-r1_R1_001_val_1.fq.gz
mr211-MV411-JQ1-r1_R2_001.fastq.gz_trimming_report.txt
mr211-MV411-JQ1-r1_R2_001_unpaired_2.fq.gz
mr211-MV411-JQ1-r1_R2_001_val_2.fq.gz
mr212-MV411-JQ1-r2_R1_001.fastq.gz_trimming_report.txt
mr212-MV411-JQ1-r2_R1_001_unpaired_1.fq.gz
mr212-MV411-JQ1-r2_R1_001_val_1.fq.gz
mr212-MV411-JQ1-r2_R2_001.fastq.gz_trimming_report.txt
mr212-MV411-JQ1-r2_R2_001_unpaired_2.fq.gz
mr212-MV411-JQ1-r2_R2_001_val_2.fq.gz
mr213-MV411-JQ1-r3_R1_001.fastq.gz_trimming_report.txt
mr213-MV411-JQ1-r3_R1_001_unpaired_1.fq.gz
mr213-MV411-JQ1-r3_R1_001_val_1.fq.gz
mr213-MV411-JQ1-r3_R2_001.fastq.gz_trimming_report.txt
mr213-MV411-JQ1-r3_R2_001_unpaired_2.fq.gz
mr213-MV411-JQ1-r3_R2_001_val_2.fq.gz
mr214-MV411-MS2_JQ1-r1_R1_001.fastq.gz_trimming_report.txt
mr214-MV411-MS2_JQ1-r1_R1_001_unpaired_1.fq.gz
mr214-MV411-MS2_JQ1-r1_R1_001_val_1.fq.gz
mr214-MV411-MS2_JQ1-r1_R2_001.fastq.gz_trimming_report.txt
mr214-MV411-MS2_JQ1-r1_R2_001_unpaired_2.fq.gz
mr214-MV411-MS2_JQ1-r1_R2_001_val_2.fq.gz
mr215-MV411-MS2_JQ1-r2_R1_001.fastq.gz_trimming_report.txt
mr215-MV411-MS2_JQ1-r2_R1_001_unpaired_1.fq.gz
mr215-MV411-MS2_JQ1-r2_R1_001_val_1.fq.gz
mr215-MV411-MS2_JQ1-r2_R2_001.fastq.gz_trimming_report.txt
mr215-MV411-MS2_JQ1-r2_R2_001_unpaired_2.fq.gz
mr215-MV411-MS2_JQ1-r2_R2_001_val_2.fq.gz
mr216-MV411-MS2_JQ1-r3_R1_001.fastq.gz_trimming_report.txt
mr216-MV411-MS2_JQ1-r3_R1_001_unpaired_1.fq.gz
mr216-MV411-MS2_JQ1-r3_R1_001_val_1.fq.gz
mr216-MV411-MS2_JQ1-r3_R2_001.fastq.gz_trimming_report.txt
mr216-MV411-MS2_JQ1-r3_R2_001_unpaired_2.fq.gz
mr216-MV411-MS2_JQ1-r3_R2_001_val_2.fq.gz
mr217-MV411-DMSO-r1_R1_001.fastq.gz_trimming_report.txt
mr217-MV411-DMSO-r1_R1_001_unpaired_1.fq.gz
mr217-MV411-DMSO-r1_R1_001_val_1.fq.gz
mr217-MV411-DMSO-r1_R2_001.fastq.gz_trimming_report.txt
mr217-MV411-DMSO-r1_R2_001_unpaired_2.fq.gz
mr217-MV411-DMSO-r1_R2_001_val_2.fq.gz
mr218-MV411-DMSO-r2_R1_001.fastq.gz_trimming_report.txt
mr218-MV411-DMSO-r2_R1_001_unpaired_1.fq.gz
mr218-MV411-DMSO-r2_R1_001_val_1.fq.gz
mr218-MV411-DMSO-r2_R2_001.fastq.gz_trimming_report.txt
mr218-MV411-DMSO-r2_R2_001_unpaired_2.fq.gz
mr218-MV411-DMSO-r2_R2_001_val_2.fq.gz
mr219-MV411-DMSO-r3_R1_001.fastq.gz_trimming_report.txt
mr219-MV411-DMSO-r3_R1_001_unpaired_1.fq.gz
mr219-MV411-DMSO-r3_R1_001_val_1.fq.gz
mr219-MV411-DMSO-r3_R2_001.fastq.gz_trimming_report.txt
mr219-MV411-DMSO-r3_R2_001_unpaired_2.fq.gz
mr219-MV411-DMSO-r3_R2_001_val_2.fq.gz

Running slamdunk

In [ ]:
#if need to download the data from sra
! mkdir ../../data/slam/MYCpaper && cd ../../data/slam/MYCpaper && fastq_dump SRR5806781 && fastq_dump SRR5806783 && fastq_dump SRR5806785 &&
fastq_dump SRR5806780 && fastq_dump SRR5806782 && fastq_dump SRR5806784 && cd -
In [32]:
folder_bams = "../../data/"+project+'/fastqs'
bams = ! ls $folder_bams/*
bams
Out[32]:
['../../data/slamseqMax/fastqs/20200827_10_MP8179_S169_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_10_MP8179_S169_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_11_MP8179_S170_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_11_MP8179_S170_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_12_MP8179_S171_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_12_MP8179_S171_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_13_MP8179_S172_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_13_MP8179_S172_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_14_MP8179_S173_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_14_MP8179_S173_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_15_MP8179_S174_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_15_MP8179_S174_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_16_MP8179_S175_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_16_MP8179_S175_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_17_MP8179_S176_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_17_MP8179_S176_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_18_MP8179_S177_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_18_MP8179_S177_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_19_MP8179_S178_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_19_MP8179_S178_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_1_MP8179_S160_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_1_MP8179_S160_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_20_MP8179_S179_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_20_MP8179_S179_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_21_MP8179_S180_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_21_MP8179_S180_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_23_MP8179_S181_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_23_MP8179_S181_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_24_MP8179_S182_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_24_MP8179_S182_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_2_MP8179_S161_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_2_MP8179_S161_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_3_MP8179_S162_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_3_MP8179_S162_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_4_MP8179_S163_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_4_MP8179_S163_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_5_MP8179_S164_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_5_MP8179_S164_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_6_MP8179_S165_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_6_MP8179_S165_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_7_MP8179_S166_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_7_MP8179_S166_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_8_MP8179_S167_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_8_MP8179_S167_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_9_MP8179_S168_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs/20200827_9_MP8179_S168_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs/mr193-MV411-MYBi_30m-r1_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr193-MV411-MYBi_30m-r1_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr193-MV411-MYBi_30m-r1_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr193-MV411-MYBi_30m-r1_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr193-MV411-MYBi_30m-r1_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr193-MV411-MYBi_30m-r1_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr194-MV411-MYBi_30m-r2_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr194-MV411-MYBi_30m-r2_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr194-MV411-MYBi_30m-r2_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr194-MV411-MYBi_30m-r2_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr194-MV411-MYBi_30m-r2_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr194-MV411-MYBi_30m-r2_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr195-MV411-MYBi_30m-r3_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr195-MV411-MYBi_30m-r3_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr195-MV411-MYBi_30m-r3_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr195-MV411-MYBi_30m-r3_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr195-MV411-MYBi_30m-r3_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr195-MV411-MYBi_30m-r3_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr196-MV411-MYBi_30m-r4_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr196-MV411-MYBi_30m-r4_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr196-MV411-MYBi_30m-r4_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr196-MV411-MYBi_30m-r4_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr196-MV411-MYBi_30m-r4_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr196-MV411-MYBi_30m-r4_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr197-MV411-PBS_30m-r1_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr197-MV411-PBS_30m-r1_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr197-MV411-PBS_30m-r1_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr197-MV411-PBS_30m-r1_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr197-MV411-PBS_30m-r1_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr197-MV411-PBS_30m-r1_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr198-MV411-PBS_30m-r2_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr198-MV411-PBS_30m-r2_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr198-MV411-PBS_30m-r2_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr198-MV411-PBS_30m-r2_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr198-MV411-PBS_30m-r2_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr198-MV411-PBS_30m-r2_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr199-MV411-PBS_30m-r3_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr199-MV411-PBS_30m-r3_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr199-MV411-PBS_30m-r3_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr199-MV411-PBS_30m-r3_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr199-MV411-PBS_30m-r3_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr199-MV411-PBS_30m-r3_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr200-MV411-PBS_30m-r4_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr200-MV411-PBS_30m-r4_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr200-MV411-PBS_30m-r4_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr200-MV411-PBS_30m-r4_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr200-MV411-PBS_30m-r4_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr200-MV411-PBS_30m-r4_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr201-MV411-MYBi_6h-r1_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr201-MV411-MYBi_6h-r1_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr201-MV411-MYBi_6h-r1_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr201-MV411-MYBi_6h-r1_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr201-MV411-MYBi_6h-r1_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr201-MV411-MYBi_6h-r1_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr202-MV411-MYBi_6h-r2_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr202-MV411-MYBi_6h-r2_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr202-MV411-MYBi_6h-r2_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr202-MV411-MYBi_6h-r2_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr202-MV411-MYBi_6h-r2_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr202-MV411-MYBi_6h-r2_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr203-MV411-MYBi_6h-r3_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr203-MV411-MYBi_6h-r3_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr203-MV411-MYBi_6h-r3_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr203-MV411-MYBi_6h-r3_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr203-MV411-MYBi_6h-r3_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr203-MV411-MYBi_6h-r3_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr204-MV411-MYBi_6h-r4_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr204-MV411-MYBi_6h-r4_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr204-MV411-MYBi_6h-r4_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr204-MV411-MYBi_6h-r4_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr204-MV411-MYBi_6h-r4_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr204-MV411-MYBi_6h-r4_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr205-MV411-PBS_6h-r1_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr205-MV411-PBS_6h-r1_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr205-MV411-PBS_6h-r1_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr205-MV411-PBS_6h-r1_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr205-MV411-PBS_6h-r1_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr205-MV411-PBS_6h-r1_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr206-MV411-PBS_6h-r2_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr206-MV411-PBS_6h-r2_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr206-MV411-PBS_6h-r2_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr206-MV411-PBS_6h-r2_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr206-MV411-PBS_6h-r2_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr206-MV411-PBS_6h-r2_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr207-MV411-PBS_6h-r3_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr207-MV411-PBS_6h-r3_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr207-MV411-PBS_6h-r3_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr207-MV411-PBS_6h-r3_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr207-MV411-PBS_6h-r3_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr207-MV411-PBS_6h-r3_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr208-MV411-MS2-r1_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr208-MV411-MS2-r1_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr208-MV411-MS2-r1_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr208-MV411-MS2-r1_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr208-MV411-MS2-r1_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr208-MV411-MS2-r1_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr209-MV411-MS2-r2_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr209-MV411-MS2-r2_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr209-MV411-MS2-r2_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr209-MV411-MS2-r2_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr209-MV411-MS2-r2_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr209-MV411-MS2-r2_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr210-MV411-MS2-r3_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr210-MV411-MS2-r3_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr210-MV411-MS2-r3_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr210-MV411-MS2-r3_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr210-MV411-MS2-r3_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr210-MV411-MS2-r3_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr211-MV411-JQ1-r1_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr211-MV411-JQ1-r1_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr211-MV411-JQ1-r1_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr211-MV411-JQ1-r1_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr211-MV411-JQ1-r1_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr211-MV411-JQ1-r1_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr212-MV411-JQ1-r2_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr212-MV411-JQ1-r2_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr212-MV411-JQ1-r2_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr212-MV411-JQ1-r2_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr212-MV411-JQ1-r2_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr212-MV411-JQ1-r2_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr213-MV411-JQ1-r3_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr213-MV411-JQ1-r3_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr213-MV411-JQ1-r3_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr213-MV411-JQ1-r3_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr213-MV411-JQ1-r3_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr213-MV411-JQ1-r3_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr214-MV411-MS2_JQ1-r1_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr214-MV411-MS2_JQ1-r1_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr214-MV411-MS2_JQ1-r1_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr214-MV411-MS2_JQ1-r1_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr214-MV411-MS2_JQ1-r1_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr214-MV411-MS2_JQ1-r1_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr215-MV411-MS2_JQ1-r2_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr215-MV411-MS2_JQ1-r2_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr215-MV411-MS2_JQ1-r2_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr215-MV411-MS2_JQ1-r2_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr215-MV411-MS2_JQ1-r2_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr215-MV411-MS2_JQ1-r2_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr216-MV411-MS2_JQ1-r3_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr216-MV411-MS2_JQ1-r3_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr216-MV411-MS2_JQ1-r3_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr216-MV411-MS2_JQ1-r3_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr216-MV411-MS2_JQ1-r3_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr216-MV411-MS2_JQ1-r3_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr217-MV411-DMSO-r1_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr217-MV411-DMSO-r1_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr217-MV411-DMSO-r1_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr217-MV411-DMSO-r1_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr217-MV411-DMSO-r1_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr217-MV411-DMSO-r1_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr218-MV411-DMSO-r2_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr218-MV411-DMSO-r2_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr218-MV411-DMSO-r2_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr218-MV411-DMSO-r2_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr218-MV411-DMSO-r2_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr218-MV411-DMSO-r2_R2_001_val_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr219-MV411-DMSO-r3_R1_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr219-MV411-DMSO-r3_R1_001_unpaired_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr219-MV411-DMSO-r3_R1_001_val_1.fq.gz',
 '../../data/slamseqMax/fastqs/mr219-MV411-DMSO-r3_R2_001.fastq.gz_trimming_report.txt',
 '../../data/slamseqMax/fastqs/mr219-MV411-DMSO-r3_R2_001_unpaired_2.fq.gz',
 '../../data/slamseqMax/fastqs/mr219-MV411-DMSO-r3_R2_001_val_2.fq.gz']
In [31]:
rename = {
"20200707_1_MP8000_S65": "mr193-MV411-MYBi_30m-r1",
"20200707_2_MP8000_S66": "mr194-MV411-MYBi_30m-r2",
"20200707_3_MP8000_S67": "mr195-MV411-MYBi_30m-r3",
"20200707_4_MP8000_S68": "mr196-MV411-MYBi_30m-r4",
"20200707_5_MP8000_S69": "mr197-MV411-PBS_30m-r1",
"20200707_6_MP8000_S70": "mr198-MV411-PBS_30m-r2",
"20200707_7_MP8000_S71": "mr199-MV411-PBS_30m-r3",
"20200707_8_MP8000_S72": "mr200-MV411-PBS_30m-r4",
"20200707_9_MP8000_S73": "mr201-MV411-MYBi_6h-r1",
"20200707_10_MP8000_S74": "mr202-MV411-MYBi_6h-r2",
"20200707_11_MP8000_S75": "mr203-MV411-MYBi_6h-r3",
"20200707_12_MP8000_S76": "mr204-MV411-MYBi_6h-r4",
"20200707_13_MP8000_S77": "mr205-MV411-PBS_6h-r1",
"20200707_14_MP8000_S78": "mr206-MV411-PBS_6h-r2",
"20200707_15_MP8000_S79": "mr207-MV411-PBS_6h-r3",
"20200703_16_MP800_S103": "mr208-MV411-MS2-r1",
"20200703_17_MP800_S104": "mr209-MV411-MS2-r2",
"20200703_18_MP800_S105": "mr210-MV411-MS2-r3",
"20200703_19_MP800_S106": "mr211-MV411-JQ1-r1",
"20200703_20_MP800_S107": "mr212-MV411-JQ1-r2",
"20200703_21_MP800_S108": "mr213-MV411-JQ1-r3",
"20200703_22_MP800_S109": "mr214-MV411-MS2_JQ1-r1",
"20200703_23_MP800_S110": "mr215-MV411-MS2_JQ1-r2",
"20200703_24_MP800_S111": "mr216-MV411-MS2_JQ1-r3",
"20200703_25_MP800_S112": "mr217-MV411-DMSO-r1",
"20200703_26_MP800_S113": "mr218-MV411-DMSO-r2",
"20200703_27_MP800_S114": "mr219-MV411-DMSO-r3",
"20200827_1_MP8179_S160": "mr252-MV411_MEF2D-DMSO_2h-r1",
"20200827_2_MP8179_S161": "mr253-MV411_MEF2D-DMSO_2h-r2",
"20200827_3_MP8179_S162": "mr254-MV411_MEF2D-DMSO_2h-r3",
"20200827_4_MP8179_S163": "mr255-MV411_MEF2D-DMSO_2h-r4",
"20200827_5_MP8179_S164": "mr256-MV411_MEF2D-VHL_2h-r1",
"20200827_6_MP8179_S165": "mr257-MV411_MEF2D-VHL_2h-r2",
"20200827_7_MP8179_S166": "mr258-MV411_MEF2D-VHL_2h-r3",
"20200827_8_MP8179_S167": "mr259-MV411_MEF2D-VHL_2h-r4",
"20200827_9_MP8179_S168": "mr260-MV411_MEF2D-DMSO_24h-r1",
"20200827_10_MP8179_S169": "mr261-MV411_MEF2D-DMSO_24h-r2",
"20200827_11_MP8179_S170": "mr262-MV411_MEF2D-DMSO_24h-r3",
"20200827_12_MP8179_S171": "mr263-MV411_MEF2D-DMSO_24h-r4",
"20200827_13_MP8179_S172": "mr264-MV411_MEF2D-VHL_24h-r1",
"20200827_14_MP8179_S173": "mr265-MV411_MEF2D-VHL_24h-r2",
"20200827_15_MP8179_S174": "mr266-MV411_MEF2D-VHL_24h-r3",
"20200827_16_MP8179_S175": "mr267-MV411_MEF2D-VHL_24h-r4",
"20200827_17_MP8179_S176": "mr268-MV411-PBS_24h-r1",
"20200827_18_MP8179_S177": "mr269-MV411-PBS_24h-r2",
"20200827_19_MP8179_S178": "mr270-MV411-PBS_24h-r3",
"20200827_20_MP8179_S179": "mr271-MV411-PBS_24h-r4",
"20200827_21_MP8179_S180": "mr272-MV411-MYBi_24h-r1",
"20200827_23_MP8179_S181": "mr273-MV411-MYBi_24h-r2",
"20200827_24_MP8179_S182": "mr274-MV411-MYBi_24h-r3",
}
In [34]:
for val in bams:
    ren  = val
    for old, new in rename.items():
        ren = ren.replace(old, new)
    if ren !=val:
        ! mv $val $ren
In [35]:
folder="../../data/"+project
folder_bams = folder+'/fastqs/'
bams = ! ls $folder_bams/*.fastq.gz
bams
Out[35]:
['../../data/slamseqMax/fastqs//mr252-MV411_MEF2D-DMSO_2h-r1_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr252-MV411_MEF2D-DMSO_2h-r1_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr253-MV411_MEF2D-DMSO_2h-r2_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr253-MV411_MEF2D-DMSO_2h-r2_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr254-MV411_MEF2D-DMSO_2h-r3_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr254-MV411_MEF2D-DMSO_2h-r3_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr255-MV411_MEF2D-DMSO_2h-r4_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr255-MV411_MEF2D-DMSO_2h-r4_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr256-MV411_MEF2D-VHL_2h-r1_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr256-MV411_MEF2D-VHL_2h-r1_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr257-MV411_MEF2D-VHL_2h-r2_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr257-MV411_MEF2D-VHL_2h-r2_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr258-MV411_MEF2D-VHL_2h-r3_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr258-MV411_MEF2D-VHL_2h-r3_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr259-MV411_MEF2D-VHL_2h-r4_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr259-MV411_MEF2D-VHL_2h-r4_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr260-MV411_MEF2D-DMSO_24h-r1_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr260-MV411_MEF2D-DMSO_24h-r1_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr261-MV411_MEF2D-DMSO_24h-r2_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr261-MV411_MEF2D-DMSO_24h-r2_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr262-MV411_MEF2D-DMSO_24h-r3_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr262-MV411_MEF2D-DMSO_24h-r3_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr263-MV411_MEF2D-DMSO_24h-r4_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr263-MV411_MEF2D-DMSO_24h-r4_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr264-MV411_MEF2D-VHL_24h-r1_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr264-MV411_MEF2D-VHL_24h-r1_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr265-MV411_MEF2D-VHL_24h-r2_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr265-MV411_MEF2D-VHL_24h-r2_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr266-MV411_MEF2D-VHL_24h-r3_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr266-MV411_MEF2D-VHL_24h-r3_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr267-MV411_MEF2D-VHL_24h-r4_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr267-MV411_MEF2D-VHL_24h-r4_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr268-MV411-PBS_24h-r1_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr268-MV411-PBS_24h-r1_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr269-MV411-PBS_24h-r2_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr269-MV411-PBS_24h-r2_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr270-MV411-PBS_24h-r3_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr270-MV411-PBS_24h-r3_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr271-MV411-PBS_24h-r4_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr271-MV411-PBS_24h-r4_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr272-MV411-MYBi_24h-r1_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr272-MV411-MYBi_24h-r1_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr273-MV411-MYBi_24h-r2_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr273-MV411-MYBi_24h-r2_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr274-MV411-MYBi_24h-r3_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr274-MV411-MYBi_24h-r3_R2_001.fastq.gz']
In [4]:
! pip3 install git+https://github.com/jkobject/slamdunk.git --upgrade
# please also install trimgalore and cutadapt
Collecting git+https://github.com/jkobject/slamdunk.git
  Cloning https://github.com/jkobject/slamdunk.git to /tmp/pip-req-build-qa580_ce
Requirement already satisfied, skipping upgrade: joblib>=0.9.4 in /home/jeremie/.local/lib/python3.8/site-packages (from slamdunk==0.4.0) (0.14.1)
Requirement already satisfied, skipping upgrade: pybedtools>=0.6.4 in /home/jeremie/.local/lib/python3.8/site-packages (from slamdunk==0.4.0) (0.8.1)
Requirement already satisfied, skipping upgrade: intervaltree>=2.1.0 in /home/jeremie/.local/lib/python3.8/site-packages (from slamdunk==0.4.0) (3.0.2)
Requirement already satisfied, skipping upgrade: pandas>=0.13.1 in /home/jeremie/.local/lib/python3.8/site-packages (from slamdunk==0.4.0) (1.0.3)
Requirement already satisfied, skipping upgrade: biopython>=1.63 in /home/jeremie/.local/lib/python3.8/site-packages (from slamdunk==0.4.0) (1.77)
Requirement already satisfied, skipping upgrade: pysam>=0.8.3 in /home/jeremie/.local/lib/python3.8/site-packages (from slamdunk==0.4.0) (0.15.4)
Requirement already satisfied, skipping upgrade: Cython>=0.20.1 in /home/jeremie/.local/lib/python3.8/site-packages (from slamdunk==0.4.0) (0.29.17)
Requirement already satisfied, skipping upgrade: six in /home/jeremie/.local/lib/python3.8/site-packages (from pybedtools>=0.6.4->slamdunk==0.4.0) (1.14.0)
Requirement already satisfied, skipping upgrade: sortedcontainers<3.0,>=2.0 in /home/jeremie/.local/lib/python3.8/site-packages (from intervaltree>=2.1.0->slamdunk==0.4.0) (2.2.2)
Requirement already satisfied, skipping upgrade: pytz>=2017.2 in /home/jeremie/.local/lib/python3.8/site-packages (from pandas>=0.13.1->slamdunk==0.4.0) (2020.1)
Requirement already satisfied, skipping upgrade: python-dateutil>=2.6.1 in /home/jeremie/.local/lib/python3.8/site-packages (from pandas>=0.13.1->slamdunk==0.4.0) (2.8.1)
Requirement already satisfied, skipping upgrade: numpy>=1.13.3 in /home/jeremie/.local/lib/python3.8/site-packages (from pandas>=0.13.1->slamdunk==0.4.0) (1.18.4)
Building wheels for collected packages: slamdunk
  Running setup.py bdist_wheel for slamdunk ... done
  Stored in directory: /tmp/pip-ephem-wheel-cache-cggtrlco/wheels/4c/b2/9c/e1153807b1571f6f12ee9761dcf5229ceee161c5c575b631fd
Successfully built slamdunk
Installing collected packages: slamdunk
  Found existing installation: slamdunk 0.4.0
    Uninstalling slamdunk-0.4.0:
      Successfully uninstalled slamdunk-0.4.0
Successfully installed slamdunk-0.4.0
In [36]:
parrun(['../../TrimGalore-0.6.5/trim_galore --paired --cores 4 --retain_unpaired -stringency 3 --illumina '+val1+ ' '+val2+' -o '+folder_bams for val1,val2 in grouped(bams,2)],2)
In [ ]:
rm fastqs/*.fastq.gz
In [23]:
ls -al ../../data/$project/fastqs
total 323740620
drwxr-xr-x 2 jeremie jeremie      20480 Jul 16 23:59 ./
drwxr-xr-x 3 jeremie jeremie       4096 Jul 16 16:48 ../
-rw-r--r-- 1 jeremie jeremie 1972661712 Jul 16 16:09 mr193-MV411-MYBi_30m-r1_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4078 Jul 16 17:28 mr193-MV411-MYBi_30m-r1_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1745221196 Jul 16 17:28 mr193-MV411-MYBi_30m-r1_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 2001846977 Jul 16 16:11 mr193-MV411-MYBi_30m-r1_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4042 Jul 16 18:04 mr193-MV411-MYBi_30m-r1_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1771675421 Jul 16 18:04 mr193-MV411-MYBi_30m-r1_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 1883635938 Jul 16 16:11 mr194-MV411-MYBi_30m-r2_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4101 Jul 16 18:03 mr194-MV411-MYBi_30m-r2_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1656441393 Jul 16 18:03 mr194-MV411-MYBi_30m-r2_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 1898121444 Jul 16 16:09 mr194-MV411-MYBi_30m-r2_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4064 Jul 16 18:03 mr194-MV411-MYBi_30m-r2_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1668987747 Jul 16 18:03 mr194-MV411-MYBi_30m-r2_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 3664144900 Jul 16 16:10 mr195-MV411-MYBi_30m-r3_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4179 Jul 16 18:16 mr195-MV411-MYBi_30m-r3_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 3226927282 Jul 16 18:16 mr195-MV411-MYBi_30m-r3_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 3716451047 Jul 16 16:10 mr195-MV411-MYBi_30m-r3_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4149 Jul 16 18:17 mr195-MV411-MYBi_30m-r3_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 3273624821 Jul 16 18:17 mr195-MV411-MYBi_30m-r3_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 1752447342 Jul 16 16:09 mr196-MV411-MYBi_30m-r4_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4123 Jul 16 18:02 mr196-MV411-MYBi_30m-r4_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1530559903 Jul 16 18:02 mr196-MV411-MYBi_30m-r4_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 1772529030 Jul 16 16:09 mr196-MV411-MYBi_30m-r4_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4075 Jul 16 18:39 mr196-MV411-MYBi_30m-r4_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1553594531 Jul 16 18:39 mr196-MV411-MYBi_30m-r4_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 2613576581 Jul 16 16:11 mr197-MV411-PBS_30m-r1_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       3987 Jul 16 18:47 mr197-MV411-PBS_30m-r1_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 2326678410 Jul 16 18:47 mr197-MV411-PBS_30m-r1_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 2630133074 Jul 16 16:10 mr197-MV411-PBS_30m-r1_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       3976 Jul 16 18:48 mr197-MV411-PBS_30m-r1_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 2341617043 Jul 16 18:48 mr197-MV411-PBS_30m-r1_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 3351245240 Jul 16 16:10 mr198-MV411-PBS_30m-r2_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4147 Jul 16 18:53 mr198-MV411-PBS_30m-r2_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 2957225726 Jul 16 18:53 mr198-MV411-PBS_30m-r2_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 3373272401 Jul 16 16:11 mr198-MV411-PBS_30m-r2_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4120 Jul 16 18:53 mr198-MV411-PBS_30m-r2_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 2973225065 Jul 16 18:53 mr198-MV411-PBS_30m-r2_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 1960596780 Jul 16 16:11 mr199-MV411-PBS_30m-r3_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4110 Jul 16 18:41 mr199-MV411-PBS_30m-r3_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1725990637 Jul 16 18:41 mr199-MV411-PBS_30m-r3_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 1979110852 Jul 16 16:10 mr199-MV411-PBS_30m-r3_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4065 Jul 16 19:19 mr199-MV411-PBS_30m-r3_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1742107228 Jul 16 19:19 mr199-MV411-PBS_30m-r3_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 2812669024 Jul 16 16:11 mr200-MV411-PBS_30m-r4_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4152 Jul 16 19:29 mr200-MV411-PBS_30m-r4_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 2476347201 Jul 16 19:29 mr200-MV411-PBS_30m-r4_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 2815436494 Jul 16 16:11 mr200-MV411-PBS_30m-r4_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4137 Jul 16 19:29 mr200-MV411-PBS_30m-r4_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 2480425633 Jul 16 19:29 mr200-MV411-PBS_30m-r4_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 1640869794 Jul 16 16:11 mr201-MV411-MYBi_6h-r1_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       3981 Jul 16 19:16 mr201-MV411-MYBi_6h-r1_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1441679301 Jul 16 19:16 mr201-MV411-MYBi_6h-r1_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 1687581392 Jul 16 16:10 mr201-MV411-MYBi_6h-r1_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       3978 Jul 16 19:17 mr201-MV411-MYBi_6h-r1_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1487580959 Jul 16 19:17 mr201-MV411-MYBi_6h-r1_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 1802713797 Jul 16 16:05 mr202-MV411-MYBi_6h-r2_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4021 Jul 16 19:18 mr202-MV411-MYBi_6h-r2_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1579927411 Jul 16 19:18 mr202-MV411-MYBi_6h-r2_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 1818642533 Jul 16 16:06 mr202-MV411-MYBi_6h-r2_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4001 Jul 16 19:58 mr202-MV411-MYBi_6h-r2_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1595008850 Jul 16 19:58 mr202-MV411-MYBi_6h-r2_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 1388870538 Jul 16 16:07 mr203-MV411-MYBi_6h-r3_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       3973 Jul 16 19:55 mr203-MV411-MYBi_6h-r3_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1222904350 Jul 16 19:55 mr203-MV411-MYBi_6h-r3_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 1393817218 Jul 16 16:10 mr203-MV411-MYBi_6h-r3_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       3943 Jul 16 19:55 mr203-MV411-MYBi_6h-r3_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1229376298 Jul 16 19:55 mr203-MV411-MYBi_6h-r3_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 1405742865 Jul 16 16:05 mr204-MV411-MYBi_6h-r4_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4080 Jul 16 19:55 mr204-MV411-MYBi_6h-r4_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1220634069 Jul 16 19:55 mr204-MV411-MYBi_6h-r4_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 1428450634 Jul 16 16:03 mr204-MV411-MYBi_6h-r4_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4036 Jul 16 19:55 mr204-MV411-MYBi_6h-r4_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1248721580 Jul 16 19:55 mr204-MV411-MYBi_6h-r4_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 1723738018 Jul 16 16:08 mr205-MV411-PBS_6h-r1_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4017 Jul 16 19:58 mr205-MV411-PBS_6h-r1_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1525341762 Jul 16 19:58 mr205-MV411-PBS_6h-r1_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 1738665340 Jul 16 16:06 mr205-MV411-PBS_6h-r1_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       3996 Jul 16 20:18 mr205-MV411-PBS_6h-r1_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1539009328 Jul 16 20:18 mr205-MV411-PBS_6h-r1_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 1935183307 Jul 16 16:04 mr206-MV411-PBS_6h-r2_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4094 Jul 16 20:20 mr206-MV411-PBS_6h-r2_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1698865919 Jul 16 20:20 mr206-MV411-PBS_6h-r2_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 1938026916 Jul 16 16:08 mr206-MV411-PBS_6h-r2_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4060 Jul 16 20:20 mr206-MV411-PBS_6h-r2_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 1702339869 Jul 16 20:20 mr206-MV411-PBS_6h-r2_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 1793762688 Jul 16 16:07 mr207-MV411-PBS_6h-r3_R1_001.fastq.gz
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-rw-r--r-- 1 jeremie jeremie 5221458520 Jul 16 16:06 mr208-MV411-MS2-r1_R1_001.fastq.gz
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-rw-r--r-- 1 jeremie jeremie 3519529968 Jul 16 22:47 mr212-MV411-JQ1-r2_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 4615295045 Jul 16 16:08 mr213-MV411-JQ1-r3_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4169 Jul 16 22:52 mr213-MV411-JQ1-r3_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 4065121374 Jul 16 22:52 mr213-MV411-JQ1-r3_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 4698448026 Jul 16 16:06 mr213-MV411-JQ1-r3_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4142 Jul 16 22:53 mr213-MV411-JQ1-r3_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 4143911322 Jul 16 22:53 mr213-MV411-JQ1-r3_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 5192687737 Jul 16 16:11 mr214-MV411-MS2_JQ1-r1_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4193 Jul 16 22:56 mr214-MV411-MS2_JQ1-r1_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 4576147106 Jul 16 22:56 mr214-MV411-MS2_JQ1-r1_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 5315271182 Jul 16 16:06 mr214-MV411-MS2_JQ1-r1_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4157 Jul 16 23:56 mr214-MV411-MS2_JQ1-r1_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 4684702188 Jul 16 23:56 mr214-MV411-MS2_JQ1-r1_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 5509754689 Jul 16 16:09 mr215-MV411-MS2_JQ1-r2_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4238 Jul 16 23:58 mr215-MV411-MS2_JQ1-r2_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 4835138491 Jul 16 23:58 mr215-MV411-MS2_JQ1-r2_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 5741983634 Jul 16 16:09 mr215-MV411-MS2_JQ1-r2_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4211 Jul 16 23:59 mr215-MV411-MS2_JQ1-r2_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 5044583239 Jul 16 23:59 mr215-MV411-MS2_JQ1-r2_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 5589321931 Jul 16 16:06 mr216-MV411-MS2_JQ1-r3_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4172 Jul 16 23:58 mr216-MV411-MS2_JQ1-r3_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 4936956685 Jul 16 23:58 mr216-MV411-MS2_JQ1-r3_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 5658383246 Jul 16 16:08 mr216-MV411-MS2_JQ1-r3_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4141 Jul 16 23:59 mr216-MV411-MS2_JQ1-r3_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 5002806305 Jul 16 23:59 mr216-MV411-MS2_JQ1-r3_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 4051640144 Jul 16 16:09 mr217-MV411-DMSO-r1_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4047 Jul 16 23:44 mr217-MV411-DMSO-r1_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 3593376280 Jul 16 23:44 mr217-MV411-DMSO-r1_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 4194658762 Jul 16 16:06 mr217-MV411-DMSO-r1_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4026 Jul 17 00:39 mr217-MV411-DMSO-r1_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 3728280128 Jul 17 00:39 mr217-MV411-DMSO-r1_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 4375154174 Jul 16 16:07 mr218-MV411-DMSO-r2_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4100 Jul 17 00:40 mr218-MV411-DMSO-r2_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 3864291280 Jul 17 00:40 mr218-MV411-DMSO-r2_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 4564711176 Jul 16 16:06 mr218-MV411-DMSO-r2_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       4076 Jul 17 00:42 mr218-MV411-DMSO-r2_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 4042600721 Jul 17 00:42 mr218-MV411-DMSO-r2_R2_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 3021404797 Jul 16 16:09 mr219-MV411-DMSO-r3_R1_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       3984 Jul 17 00:30 mr219-MV411-DMSO-r3_R1_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 2676601777 Jul 17 00:30 mr219-MV411-DMSO-r3_R1_001_trimmed.fq.gz
-rw-r--r-- 1 jeremie jeremie 3081595402 Jul 16 16:07 mr219-MV411-DMSO-r3_R2_001.fastq.gz
-rw-r--r-- 1 jeremie jeremie       3968 Jul 17 00:31 mr219-MV411-DMSO-r3_R2_001.fastq.gz_trimming_report.txt
-rw-r--r-- 1 jeremie jeremie 2732365180 Jul 17 00:31 mr219-MV411-DMSO-r3_R2_001_trimmed.fq.gz
In [37]:
# using an ERCC ref genome (you can just append ERCC fasta to the hg38 fasta)
refgenome="../../data/ref/Homo_sapiens_assembly38_ERCC92.fasta"
In [44]:
bams
Out[44]:
['../../data/slamseqMax/fastqs//mr252-MV411_MEF2D-DMSO_2h-r1_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr252-MV411_MEF2D-DMSO_2h-r1_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr253-MV411_MEF2D-DMSO_2h-r2_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr253-MV411_MEF2D-DMSO_2h-r2_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr254-MV411_MEF2D-DMSO_2h-r3_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr254-MV411_MEF2D-DMSO_2h-r3_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr255-MV411_MEF2D-DMSO_2h-r4_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr255-MV411_MEF2D-DMSO_2h-r4_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr256-MV411_MEF2D-VHL_2h-r1_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr256-MV411_MEF2D-VHL_2h-r1_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr257-MV411_MEF2D-VHL_2h-r2_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr257-MV411_MEF2D-VHL_2h-r2_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr258-MV411_MEF2D-VHL_2h-r3_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr258-MV411_MEF2D-VHL_2h-r3_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr259-MV411_MEF2D-VHL_2h-r4_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr259-MV411_MEF2D-VHL_2h-r4_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr260-MV411_MEF2D-DMSO_24h-r1_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr260-MV411_MEF2D-DMSO_24h-r1_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr261-MV411_MEF2D-DMSO_24h-r2_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr261-MV411_MEF2D-DMSO_24h-r2_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr262-MV411_MEF2D-DMSO_24h-r3_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr262-MV411_MEF2D-DMSO_24h-r3_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr263-MV411_MEF2D-DMSO_24h-r4_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr263-MV411_MEF2D-DMSO_24h-r4_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr264-MV411_MEF2D-VHL_24h-r1_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr264-MV411_MEF2D-VHL_24h-r1_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr265-MV411_MEF2D-VHL_24h-r2_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr265-MV411_MEF2D-VHL_24h-r2_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr266-MV411_MEF2D-VHL_24h-r3_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr266-MV411_MEF2D-VHL_24h-r3_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr267-MV411_MEF2D-VHL_24h-r4_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr267-MV411_MEF2D-VHL_24h-r4_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr268-MV411-PBS_24h-r1_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr268-MV411-PBS_24h-r1_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr269-MV411-PBS_24h-r2_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr269-MV411-PBS_24h-r2_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr270-MV411-PBS_24h-r3_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr270-MV411-PBS_24h-r3_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr271-MV411-PBS_24h-r4_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr271-MV411-PBS_24h-r4_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr272-MV411-MYBi_24h-r1_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr272-MV411-MYBi_24h-r1_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr273-MV411-MYBi_24h-r2_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr273-MV411-MYBi_24h-r2_R2_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr274-MV411-MYBi_24h-r3_R1_001.fastq.gz',
 '../../data/slamseqMax/fastqs//mr274-MV411-MYBi_24h-r3_R2_001.fastq.gz']
In [46]:
# we are doing it paired end
parrun(['slamdunk all -r '+refgenome+' -b ../data/Muhar_Slamseq/GSE100708_hg38_refseq_062016_ensemblv84_3UTR.bed \
    -o ../../data/'+project+'/res/ -t 8 -c 2 -N '+val1.split('/')[-1].split('_R')[0]+' '+val1.replace('.fastq.gz','_val_1.fq.gz')+" "+val2.replace('.fastq.gz','_val_2.fq.gz') for val1,val2 in grouped(bams[4:],2)], 2)
In [47]:
ls ../../data/$project/res/count/*.tsv
../../data/slamseqMax/res/count/mr252-MV411_MEF2D-DMSO_2h-r1_tcount.tsv
../../data/slamseqMax/res/count/mr253-MV411_MEF2D-DMSO_2h-r2_tcount.tsv
../../data/slamseqMax/res/count/mr254-MV411_MEF2D-DMSO_2h-r3_tcount.tsv
../../data/slamseqMax/res/count/mr255-MV411_MEF2D-DMSO_2h-r4_tcount.tsv
../../data/slamseqMax/res/count/mr256-MV411_MEF2D-VHL_2h-r1_tcount.tsv
../../data/slamseqMax/res/count/mr257-MV411_MEF2D-VHL_2h-r2_tcount.tsv
../../data/slamseqMax/res/count/mr258-MV411_MEF2D-VHL_2h-r3_tcount.tsv
../../data/slamseqMax/res/count/mr259-MV411_MEF2D-VHL_2h-r4_tcount.tsv
../../data/slamseqMax/res/count/mr260-MV411_MEF2D-DMSO_24h-r1_tcount.tsv
../../data/slamseqMax/res/count/mr261-MV411_MEF2D-DMSO_24h-r2_tcount.tsv
../../data/slamseqMax/res/count/mr262-MV411_MEF2D-DMSO_24h-r3_tcount.tsv
../../data/slamseqMax/res/count/mr263-MV411_MEF2D-DMSO_24h-r4_tcount.tsv
../../data/slamseqMax/res/count/mr264-MV411_MEF2D-VHL_24h-r1_tcount.tsv
../../data/slamseqMax/res/count/mr265-MV411_MEF2D-VHL_24h-r2_tcount.tsv
../../data/slamseqMax/res/count/mr266-MV411_MEF2D-VHL_24h-r3_tcount.tsv
../../data/slamseqMax/res/count/mr267-MV411_MEF2D-VHL_24h-r4_tcount.tsv
../../data/slamseqMax/res/count/mr268-MV411-PBS_24h-r1_tcount.tsv
../../data/slamseqMax/res/count/mr269-MV411-PBS_24h-r2_tcount.tsv
../../data/slamseqMax/res/count/mr270-MV411-PBS_24h-r3_tcount.tsv
../../data/slamseqMax/res/count/mr271-MV411-PBS_24h-r4_tcount.tsv
../../data/slamseqMax/res/count/mr272-MV411-MYBi_24h-r1_tcount.tsv
../../data/slamseqMax/res/count/mr273-MV411-MYBi_24h-r2_tcount.tsv
../../data/slamseqMax/res/count/mr274-MV411-MYBi_24h-r3_tcount.tsv

we first need to recreate out RNA matrix from slamdunk's tcount files

In [358]:
!gsutil -m cp -r ../../data/$project/* gs://amlproject/RNA/slamseq_iBet_max/
Copying file://../../data/slamseqMax/fastqs/mr206-MV411-PBS_6h-r2_R2_001_unpaired_2.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr196-MV411-MYBi_30m-r4_R1_001.fastq.gz_trimming_report.txt [Content-Type=text/plain]...
Copying file://../../data/slamseqMax/fastqs/mr212-MV411-JQ1-r2_R2_001.fastq.gz_trimming_report.txt [Content-Type=text/plain]...
Copying file://../../data/slamseqMax/fastqs/mr209-MV411-MS2-r2_R1_001.fastq.gz_trimming_report.txt [Content-Type=text/plain]...
Copying file://../../data/slamseqMax/fastqs/mr193-MV411-MYBi_30m-r1_R1_001.fastq.gz_trimming_report.txt [Content-Type=text/plain]...
Copying file://../../data/slamseqMax/fastqs/mr195-MV411-MYBi_30m-r3_R1_001_val_1.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr200-MV411-PBS_30m-r4_R2_001_val_2.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr207-MV411-PBS_6h-r3_R1_001_unpaired_1.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr193-MV411-MYBi_30m-r1_R2_001.fastq.gz_trimming_report.txt [Content-Type=text/plain]...
Copying file://../../data/slamseqMax/fastqs/mr211-MV411-JQ1-r1_R2_001_unpaired_2.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr195-MV411-MYBi_30m-r3_R2_001_unpaired_2.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr217-MV411-DMSO-r1_R2_001.fastq.gz_trimming_report.txt [Content-Type=text/plain]...
==> NOTE: You are uploading one or more large file(s), which would run          
significantly faster if you enable parallel composite uploads. This
feature can be enabled by editing the
"parallel_composite_upload_threshold" value in your .boto
configuration file. However, note that if you do this large files will
be uploaded as `composite objects
<https://cloud.google.com/storage/docs/composite-objects>`_,which
means that any user who downloads such objects will need to have a
compiled crcmod installed (see "gsutil help crcmod"). This is because
without a compiled crcmod, computing checksums on composite objects is
so slow that gsutil disables downloads of composite objects.

Copying file://../../data/slamseqMax/fastqs/mr196-MV411-MYBi_30m-r4_R2_001.fastq.gz_trimming_report.txt [Content-Type=text/plain]...
Copying file://../../data/slamseqMax/fastqs/mr210-MV411-MS2-r3_R1_001_unpaired_1.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr194-MV411-MYBi_30m-r2_R2_001_unpaired_2.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr204-MV411-MYBi_6h-r4_R2_001.fastq.gz_trimming_report.txt [Content-Type=text/plain]...
Copying file://../../data/slamseqMax/fastqs/mr217-MV411-DMSO-r1_R1_001_val_1.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr200-MV411-PBS_30m-r4_R1_001_unpaired_1.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr201-MV411-MYBi_6h-r1_R1_001_val_1.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr207-MV411-PBS_6h-r3_R2_001.fastq.gz_trimming_report.txt [Content-Type=text/plain]...
Copying file://../../data/slamseqMax/fastqs/mr193-MV411-MYBi_30m-r1_R2_001_unpaired_2.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr206-MV411-PBS_6h-r2_R1_001_val_1.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr199-MV411-PBS_30m-r3_R2_001_val_2.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr211-MV411-JQ1-r1_R2_001.fastq.gz_trimming_report.txt [Content-Type=text/plain]...
Copying file://../../data/slamseqMax/fastqs/mr217-MV411-DMSO-r1_R1_001_unpaired_1.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr193-MV411-MYBi_30m-r1_R1_001_unpaired_1.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr194-MV411-MYBi_30m-r2_R1_001_unpaired_1.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr215-MV411-MS2_JQ1-r2_R1_001_unpaired_1.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr204-MV411-MYBi_6h-r4_R2_001_val_2.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr215-MV411-MS2_JQ1-r2_R1_001.fastq.gz_trimming_report.txt [Content-Type=text/plain]...
Copying file://../../data/slamseqMax/fastqs/mr211-MV411-JQ1-r1_R1_001_val_1.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr194-MV411-MYBi_30m-r2_R1_001.fastq.gz_trimming_report.txt [Content-Type=text/plain]...
Copying file://../../data/slamseqMax/fastqs/mr207-MV411-PBS_6h-r3_R1_001.fastq.gz_trimming_report.txt [Content-Type=text/plain]...
Copying file://../../data/slamseqMax/fastqs/mr194-MV411-MYBi_30m-r2_R2_001_val_2.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr202-MV411-MYBi_6h-r2_R1_001_val_1.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr213-MV411-JQ1-r3_R2_001_val_2.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr196-MV411-MYBi_30m-r4_R1_001_unpaired_1.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr197-MV411-PBS_30m-r1_R1_001_unpaired_1.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr194-MV411-MYBi_30m-r2_R2_001.fastq.gz_trimming_report.txt [Content-Type=text/plain]...
Copying file://../../data/slamseqMax/fastqs/mr200-MV411-PBS_30m-r4_R1_001_val_1.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr204-MV411-MYBi_6h-r4_R2_001_unpaired_2.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr197-MV411-PBS_30m-r1_R2_001_val_2.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr198-MV411-PBS_30m-r2_R1_001_unpaired_1.fq.gz [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/fastqs/mr199-MV411-PBS_30m-r3_R1_001.fastq.gz_trimming_report.txt [Content-Type=text/plain]...
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Copying file://../../data/slamseqMax/res/filter/mr206-MV411-PBS_6h-r2_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr203-MV411-MYBi_6h-r3_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr214-MV411-MS2_JQ1-r1_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr214-MV411-MS2_JQ1-r1_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr206-MV411-PBS_6h-r2_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr211-MV411-JQ1-r1_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr206-MV411-PBS_6h-r2_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr195-MV411-MYBi_30m-r3_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr219-MV411-DMSO-r3_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr216-MV411-MS2_JQ1-r3_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr202-MV411-MYBi_6h-r2_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr198-MV411-PBS_30m-r2_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr207-MV411-PBS_6h-r3_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr201-MV411-MYBi_6h-r1_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr217-MV411-DMSO-r1_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr208-MV411-MS2-r1_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr208-MV411-MS2-r1_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr205-MV411-PBS_6h-r1_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr217-MV411-DMSO-r1_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr204-MV411-MYBi_6h-r4_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr196-MV411-MYBi_30m-r4_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr194-MV411-MYBi_30m-r2_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr195-MV411-MYBi_30m-r3_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr214-MV411-MS2_JQ1-r1_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr198-MV411-PBS_30m-r2_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr213-MV411-JQ1-r3_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr199-MV411-PBS_30m-r3_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr201-MV411-MYBi_6h-r1_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr211-MV411-JQ1-r1_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr210-MV411-MS2-r3_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr197-MV411-PBS_30m-r1_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr215-MV411-MS2_JQ1-r2_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr202-MV411-MYBi_6h-r2_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr203-MV411-MYBi_6h-r3_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr211-MV411-JQ1-r1_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr201-MV411-MYBi_6h-r1_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr200-MV411-PBS_30m-r4_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr199-MV411-PBS_30m-r3_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr200-MV411-PBS_30m-r4_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr200-MV411-PBS_30m-r4_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr195-MV411-MYBi_30m-r3_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr212-MV411-JQ1-r2_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr207-MV411-PBS_6h-r3_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr208-MV411-MS2-r1_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr204-MV411-MYBi_6h-r4_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr194-MV411-MYBi_30m-r2_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr212-MV411-JQ1-r2_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr210-MV411-MS2-r3_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr215-MV411-MS2_JQ1-r2_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr193-MV411-MYBi_30m-r1_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr198-MV411-PBS_30m-r2_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr209-MV411-MS2-r2_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr205-MV411-PBS_6h-r1_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr203-MV411-MYBi_6h-r3_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr202-MV411-MYBi_6h-r2_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr213-MV411-JQ1-r3_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr218-MV411-DMSO-r2_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr212-MV411-JQ1-r2_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr210-MV411-MS2-r3_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr219-MV411-DMSO-r3_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr196-MV411-MYBi_30m-r4_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr199-MV411-PBS_30m-r3_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr205-MV411-PBS_6h-r1_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr217-MV411-DMSO-r1_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr209-MV411-MS2-r2_filtered.bam [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr218-MV411-DMSO-r2_filtered.log [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr193-MV411-MYBi_30m-r1_filtered.bam.bai [Content-Type=application/octet-stream]...
Copying file://../../data/slamseqMax/res/filter/mr213-MV411-JQ1-r3_filtered.log [Content-Type=application/octet-stream]...
| [415/415 files][305.7 GiB/305.7 GiB] 100% Done 109.3 MiB/s ETA 00:00:00       
Operation completed over 415 objects/305.7 GiB.                                  

Getting counts over ERCC genome

In [73]:
counts = {}
folder = "../../data/slamseqMax/res/filter"
files = ! ls $folder/mr*
files = [file.split('/')[-1] for file in files if file.endswith(".bam")]
In [74]:
files
Out[74]:
['mr252-MV411_MEF2D-DMSO_2h-r1_filtered.bam',
 'mr253-MV411_MEF2D-DMSO_2h-r2_filtered.bam',
 'mr254-MV411_MEF2D-DMSO_2h-r3_filtered.bam',
 'mr255-MV411_MEF2D-DMSO_2h-r4_filtered.bam',
 'mr256-MV411_MEF2D-VHL_2h-r1_filtered.bam',
 'mr257-MV411_MEF2D-VHL_2h-r2_filtered.bam',
 'mr258-MV411_MEF2D-VHL_2h-r3_filtered.bam',
 'mr259-MV411_MEF2D-VHL_2h-r4_filtered.bam',
 'mr260-MV411_MEF2D-DMSO_24h-r1_filtered.bam',
 'mr261-MV411_MEF2D-DMSO_24h-r2_filtered.bam',
 'mr262-MV411_MEF2D-DMSO_24h-r3_filtered.bam',
 'mr263-MV411_MEF2D-DMSO_24h-r4_filtered.bam',
 'mr264-MV411_MEF2D-VHL_24h-r1_filtered.bam',
 'mr265-MV411_MEF2D-VHL_24h-r2_filtered.bam',
 'mr266-MV411_MEF2D-VHL_24h-r3_filtered.bam',
 'mr267-MV411_MEF2D-VHL_24h-r4_filtered.bam',
 'mr268-MV411-PBS_24h-r1_filtered.bam',
 'mr269-MV411-PBS_24h-r2_filtered.bam',
 'mr270-MV411-PBS_24h-r3_filtered.bam',
 'mr271-MV411-PBS_24h-r4_filtered.bam',
 'mr272-MV411-MYBi_24h-r1_filtered.bam',
 'mr273-MV411-MYBi_24h-r2_filtered.bam',
 'mr274-MV411-MYBi_24h-r3_filtered.bam']
In [64]:
parrun(["samtools view -hb "+folder+"/"+f+" ERCC-00002 ERCC-00003 ERCC-00004 ERCC-00009 ERCC-00012 ERCC-00013 ERCC-00014 ERCC-00016 ERCC-00017 ERCC-00019 ERCC-00022 ERCC-00024 ERCC-00025 ERCC-00028 ERCC-00031 ERCC-00033 ERCC-00034 ERCC-00035 ERCC-00039 ERCC-00040 ERCC-00041 ERCC-00042 ERCC-00043 ERCC-00044 ERCC-00046 ERCC-00048 ERCC-00051 ERCC-00053 ERCC-00054 ERCC-00057 ERCC-00058 ERCC-00059 ERCC-00060 ERCC-00061 ERCC-00062 ERCC-00067 ERCC-00069 ERCC-00071 ERCC-00073 ERCC-00074 ERCC-00075 ERCC-00076 ERCC-00077 ERCC-00078 ERCC-00079 ERCC-00081 ERCC-00083 ERCC-00084 ERCC-00085 ERCC-00086 ERCC-00092 ERCC-00095 ERCC-00096 ERCC-00097 ERCC-00098 ERCC-00099 ERCC-00104 ERCC-00108 ERCC-00109 ERCC-00111 ERCC-00112 ERCC-00113 ERCC-00116 ERCC-00117 ERCC-00120 ERCC-00123 ERCC-00126 ERCC-00130 ERCC-00131 ERCC-00134 ERCC-00136 ERCC-00137 ERCC-00138 ERCC-00142 ERCC-00143 ERCC-00144 ERCC-00145 ERCC-00147 ERCC-00148 ERCC-00150 ERCC-00154 ERCC-00156 ERCC-00157 ERCC-00158 ERCC-00160 ERCC-00162 ERCC-00163 ERCC-00164 ERCC-00165 ERCC-00168 ERCC-00170 ERCC-00171 > "+folder+"/ERCC_"+f for f in files],cores=10)
In [65]:
parrun(["bedtools genomecov -ibam "+folder+"/ERCC_"+f+" > "+folder+"/"+f+".bed" for f in files],cores=10)
In [67]:
ERCC = ["ERCC-00002", "ERCC-00003", "ERCC-00004", "ERCC-00009", "ERCC-00012", "ERCC-00013", "ERCC-00014", "ERCC-00016", "ERCC-00017", "ERCC-00019", "ERCC-00022", "ERCC-00024", "ERCC-00025", "ERCC-00028", "ERCC-00031", "ERCC-00033", "ERCC-00034", "ERCC-00035", "ERCC-00039", "ERCC-00040", "ERCC-00041", "ERCC-00042", "ERCC-00043", "ERCC-00044", "ERCC-00046", "ERCC-00048", "ERCC-00051", "ERCC-00053", "ERCC-00054", "ERCC-00057", "ERCC-00058", "ERCC-00059", "ERCC-00060", "ERCC-00061", "ERCC-00062", "ERCC-00067", "ERCC-00069", "ERCC-00071", "ERCC-00073", "ERCC-00074", "ERCC-00075", "ERCC-00076", "ERCC-00077", "ERCC-00078", "ERCC-00079", "ERCC-00081", "ERCC-00083", "ERCC-00084", "ERCC-00085", "ERCC-00086", "ERCC-00092", "ERCC-00095", "ERCC-00096", "ERCC-00097", "ERCC-00098", "ERCC-00099", "ERCC-00104", "ERCC-00108", "ERCC-00109", "ERCC-00111", "ERCC-00112", "ERCC-00113", "ERCC-00116", "ERCC-00117", "ERCC-00120", "ERCC-00123", "ERCC-00126", "ERCC-00130", "ERCC-00131", "ERCC-00134", "ERCC-00136", "ERCC-00137", "ERCC-00138", "ERCC-00142", "ERCC-00143", "ERCC-00144", "ERCC-00145", "ERCC-00147", "ERCC-00148", "ERCC-00150", "ERCC-00154", "ERCC-00156", "ERCC-00157", "ERCC-00158", "ERCC-00160", "ERCC-00162", "ERCC-00163", "ERCC-00164", "ERCC-00165", "ERCC-00168", "ERCC-00170", "ERCC-00171"]
res  = {i:[] for i in files}
for val in files:
    cov = pd.read_csv(folder+"/"+val+".bed",sep="\t",header=None)
    for i in ERCC:
        res[val].append(cov[cov[0]==i][1].mean())
df = pd.DataFrame(data=res,index=ERCC)
In [79]:
ls ../../data/slamseqMax/res/filter/mr*.bam
../../data/slamseqMax/res/filter/mr252-MV411_MEF2D-DMSO_2h-r1_filtered.bam
../../data/slamseqMax/res/filter/mr253-MV411_MEF2D-DMSO_2h-r2_filtered.bam
../../data/slamseqMax/res/filter/mr254-MV411_MEF2D-DMSO_2h-r3_filtered.bam
../../data/slamseqMax/res/filter/mr255-MV411_MEF2D-DMSO_2h-r4_filtered.bam
../../data/slamseqMax/res/filter/mr256-MV411_MEF2D-VHL_2h-r1_filtered.bam
../../data/slamseqMax/res/filter/mr257-MV411_MEF2D-VHL_2h-r2_filtered.bam
../../data/slamseqMax/res/filter/mr258-MV411_MEF2D-VHL_2h-r3_filtered.bam
../../data/slamseqMax/res/filter/mr259-MV411_MEF2D-VHL_2h-r4_filtered.bam
../../data/slamseqMax/res/filter/mr260-MV411_MEF2D-DMSO_24h-r1_filtered.bam
../../data/slamseqMax/res/filter/mr261-MV411_MEF2D-DMSO_24h-r2_filtered.bam
../../data/slamseqMax/res/filter/mr262-MV411_MEF2D-DMSO_24h-r3_filtered.bam
../../data/slamseqMax/res/filter/mr263-MV411_MEF2D-DMSO_24h-r4_filtered.bam
../../data/slamseqMax/res/filter/mr264-MV411_MEF2D-VHL_24h-r1_filtered.bam
../../data/slamseqMax/res/filter/mr265-MV411_MEF2D-VHL_24h-r2_filtered.bam
../../data/slamseqMax/res/filter/mr266-MV411_MEF2D-VHL_24h-r3_filtered.bam
../../data/slamseqMax/res/filter/mr267-MV411_MEF2D-VHL_24h-r4_filtered.bam
../../data/slamseqMax/res/filter/mr268-MV411-PBS_24h-r1_filtered.bam
../../data/slamseqMax/res/filter/mr269-MV411-PBS_24h-r2_filtered.bam
../../data/slamseqMax/res/filter/mr270-MV411-PBS_24h-r3_filtered.bam
../../data/slamseqMax/res/filter/mr271-MV411-PBS_24h-r4_filtered.bam
../../data/slamseqMax/res/filter/mr272-MV411-MYBi_24h-r1_filtered.bam
../../data/slamseqMax/res/filter/mr273-MV411-MYBi_24h-r2_filtered.bam
../../data/slamseqMax/res/filter/mr274-MV411-MYBi_24h-r3_filtered.bam
In [80]:
totalcounts = ! for unkn in $(ls ../../data/slamseqMax/res/filter/mr*.bam); do samtools view -c -F 260 $unkn; done
In [81]:
totalcounts
Out[81]:
['../../data/slamseqMax/res/filter/mr252-MV411_MEF2D-DMSO_2h-r1_filtered.bam',
 '87120807',
 '../../data/slamseqMax/res/filter/mr253-MV411_MEF2D-DMSO_2h-r2_filtered.bam',
 '83131772',
 '../../data/slamseqMax/res/filter/mr254-MV411_MEF2D-DMSO_2h-r3_filtered.bam',
 '169547340',
 '../../data/slamseqMax/res/filter/mr255-MV411_MEF2D-DMSO_2h-r4_filtered.bam',
 '162737874',
 '../../data/slamseqMax/res/filter/mr256-MV411_MEF2D-VHL_2h-r1_filtered.bam',
 '60636179',
 '../../data/slamseqMax/res/filter/mr257-MV411_MEF2D-VHL_2h-r2_filtered.bam',
 '101791667',
 '../../data/slamseqMax/res/filter/mr258-MV411_MEF2D-VHL_2h-r3_filtered.bam',
 '149282005',
 '../../data/slamseqMax/res/filter/mr259-MV411_MEF2D-VHL_2h-r4_filtered.bam',
 '130879596',
 '../../data/slamseqMax/res/filter/mr260-MV411_MEF2D-DMSO_24h-r1_filtered.bam',
 '204252217',
 '../../data/slamseqMax/res/filter/mr261-MV411_MEF2D-DMSO_24h-r2_filtered.bam',
 '74266908',
 '../../data/slamseqMax/res/filter/mr262-MV411_MEF2D-DMSO_24h-r3_filtered.bam',
 '124166412',
 '../../data/slamseqMax/res/filter/mr263-MV411_MEF2D-DMSO_24h-r4_filtered.bam',
 '109829880',
 '../../data/slamseqMax/res/filter/mr264-MV411_MEF2D-VHL_24h-r1_filtered.bam',
 '79024803',
 '../../data/slamseqMax/res/filter/mr265-MV411_MEF2D-VHL_24h-r2_filtered.bam',
 '126029299',
 '../../data/slamseqMax/res/filter/mr266-MV411_MEF2D-VHL_24h-r3_filtered.bam',
 '93542923',
 '../../data/slamseqMax/res/filter/mr267-MV411_MEF2D-VHL_24h-r4_filtered.bam',
 '107586723',
 '../../data/slamseqMax/res/filter/mr268-MV411-PBS_24h-r1_filtered.bam',
 '85905103',
 '../../data/slamseqMax/res/filter/mr269-MV411-PBS_24h-r2_filtered.bam',
 '31694204',
 '../../data/slamseqMax/res/filter/mr270-MV411-PBS_24h-r3_filtered.bam',
 '128780021',
 '../../data/slamseqMax/res/filter/mr271-MV411-PBS_24h-r4_filtered.bam',
 '37635249',
 '../../data/slamseqMax/res/filter/mr272-MV411-MYBi_24h-r1_filtered.bam',
 '36638284',
 '../../data/slamseqMax/res/filter/mr273-MV411-MYBi_24h-r2_filtered.bam',
 '75047033',
 '../../data/slamseqMax/res/filter/mr274-MV411-MYBi_24h-r3_filtered.bam',
 '83424257']
In [84]:
totalcounts= [
52834953,
48661773,
99303819,
45979870,
71673717,
90428614,
51950460,
75989518,
41520582,
44914503,
34919910,
34840133,
44955360,
50106552,
47137700,
148549270,
103180767,
160756237,
128740743,
109673222,
130928802,
147257131,
149990181,
155634820,
116426167,
124950994,
86078120,
87120807,
83131772,
169547340,
162737874,
60636179,
101791667,
149282005,
130879596,
204252217,
74266908,
124166412,
109829880,
79024803,
126029299,
93542923,
107586723,
85905103,
31694204,
128780021,
37635249,
36638284,
75047033,
83424257]
In [176]:
res = 10000*df.mean()/totalcounts[-23:]
In [177]:
res
Out[177]:
mr252-MV411_MEF2D-DMSO_2h-r1_filtered.bam     0.220618
mr253-MV411_MEF2D-DMSO_2h-r2_filtered.bam     0.234046
mr254-MV411_MEF2D-DMSO_2h-r3_filtered.bam     0.251439
mr255-MV411_MEF2D-DMSO_2h-r4_filtered.bam     0.191159
mr256-MV411_MEF2D-VHL_2h-r1_filtered.bam      0.225943
mr257-MV411_MEF2D-VHL_2h-r2_filtered.bam      0.226751
mr258-MV411_MEF2D-VHL_2h-r3_filtered.bam      0.256114
mr259-MV411_MEF2D-VHL_2h-r4_filtered.bam      0.231022
mr260-MV411_MEF2D-DMSO_24h-r1_filtered.bam    0.149643
mr261-MV411_MEF2D-DMSO_24h-r2_filtered.bam    0.131132
mr262-MV411_MEF2D-DMSO_24h-r3_filtered.bam    0.143506
mr263-MV411_MEF2D-DMSO_24h-r4_filtered.bam    0.137635
mr264-MV411_MEF2D-VHL_24h-r1_filtered.bam     0.158762
mr265-MV411_MEF2D-VHL_24h-r2_filtered.bam     0.176088
mr266-MV411_MEF2D-VHL_24h-r3_filtered.bam     0.263525
mr267-MV411_MEF2D-VHL_24h-r4_filtered.bam     0.185894
mr268-MV411-PBS_24h-r1_filtered.bam           0.270967
mr269-MV411-PBS_24h-r2_filtered.bam           0.322324
mr270-MV411-PBS_24h-r3_filtered.bam           0.183615
mr271-MV411-PBS_24h-r4_filtered.bam           0.164630
mr272-MV411-MYBi_24h-r1_filtered.bam          1.131675
mr273-MV411-MYBi_24h-r2_filtered.bam          0.819142
mr274-MV411-MYBi_24h-r3_filtered.bam          1.061710
dtype: float64
In [90]:
prev=0
r={}
for val in [4,4,4,3,3,3,3,3,4,4,4,4,4,3][-6:]:
    r[res.keys()[prev].split('-')[2]]=[np.mean(res[prev:prev+val]), np.var(res[prev:prev+val])**(1/2)]
    prev+=val
In [91]:
r
Out[91]:
{'DMSO_2h': [0.2243153232470735, 0.02204177171648129],
 'VHL_2h': [0.23495725535742493, 0.012366178880134462],
 'DMSO_24h': [0.14047889898493598, 0.0068663572605201255],
 'VHL_24h': [0.1960673739532328, 0.04013998428238451],
 'PBS_24h': [0.23538398133738964, 0.06424715552832781],
 'MYBi_24h': [1.0041758119681277, 0.13391993501133953]}
In [92]:
d= pd.DataFrame(data=r.values(),index=r.keys(), columns=['ERCC pseudo-counts','var'])
d['Experiments']=d.index
sns.barplot("Experiments","ERCC pseudo-counts",data=d,ci=None,)
plt.errorbar(x=range(0,len(d)),y=d['ERCC pseudo-counts'],
            yerr=d['var'], fmt='none', c= 'r')
plt.xticks(rotation=60,ha='right')
plt.savefig('../results/'+project+"/plots/"+version+"_scaling_fact_with_conf.pdf")
In [93]:
location= '../../data/'+project+'/res/count/'
mincount_toremove=5
minvar_toremove=0
In [94]:
readcounts, tccounts = readFromSlamdunk(loc=location,minvar_toremove=minvar_toremove, mincount_toremove=mincount_toremove)
found 23 files:dict_keys(['mr270-MV411-PBS_24h-r3_tcount', 'mr268-MV411-PBS_24h-r1_tcount', 'mr272-MV411-MYBi_24h-r1_tcount', 'mr269-MV411-PBS_24h-r2_tcount', 'mr263-MV411_MEF2D-DMSO_24h-r4_tcount', 'mr257-MV411_MEF2D-VHL_2h-r2_tcount', 'mr266-MV411_MEF2D-VHL_24h-r3_tcount', 'mr258-MV411_MEF2D-VHL_2h-r3_tcount', 'mr255-MV411_MEF2D-DMSO_2h-r4_tcount', 'mr259-MV411_MEF2D-VHL_2h-r4_tcount', 'mr253-MV411_MEF2D-DMSO_2h-r2_tcount', 'mr261-MV411_MEF2D-DMSO_24h-r2_tcount', 'mr256-MV411_MEF2D-VHL_2h-r1_tcount', 'mr254-MV411_MEF2D-DMSO_2h-r3_tcount', 'mr264-MV411_MEF2D-VHL_24h-r1_tcount', 'mr262-MV411_MEF2D-DMSO_24h-r3_tcount', 'mr267-MV411_MEF2D-VHL_24h-r4_tcount', 'mr265-MV411_MEF2D-VHL_24h-r2_tcount', 'mr273-MV411-MYBi_24h-r2_tcount', 'mr271-MV411-PBS_24h-r4_tcount', 'mr274-MV411-MYBi_24h-r3_tcount', 'mr260-MV411_MEF2D-DMSO_24h-r1_tcount', 'mr252-MV411_MEF2D-DMSO_2h-r1_tcount'])
2023 538
[772, 243] [12, 5]
787 93
[709, 174] [2, 0]
97 3
[533, 126] [4, 0]
250 33
[295, 50] [0, 0]
2341 440
[621, 194] [1, 1]
556 148
[815, 209] [2, 0]
305 36
[468, 129] [0, 0]
1595 423
[1054, 244] [7, 0]
4857 2222
[958, 277] [7, 6]
3671 1891
[712, 221] [17, 5]
1688 530
[566, 148] [5, 1]
773 49
[551, 108] [1, 0]
1321 543
[441, 120] [4, 0]
5287 2163
[999, 303] [10, 3]
768 187
[285, 74] [5, 1]
2185 420
[661, 198] [6, 1]
503 61
[532, 132] [1, 0]
1656 532
[379, 114] [2, 2]
809 22
[708, 149] [4, 0]
153 19
[456, 110] [4, 0]
744 17
[1038, 139] [0, 0]
4751 861
[1176, 373] [9, 3]
2177 721
[534, 160] [5, 0]
you need access to taiga for this (https://pypi.org/project/taigapy/)
1118 could not be parsed... we don't have all genes already
you need access to taiga for this (https://pypi.org/project/taigapy/)
1118 could not be parsed... we don't have all genes already

SLAM-seq

All SLAM-seq assays were performed at 60-70% confluency for adherent cells or 60% of the maximum cell density counted on a hemocytometer for suspension cells. 5-7h prior to each assay, growth medium was aspirated and replaced. Unless stated otherwise, cells were pre-treated with indicated small molecule inhibitors or 100µM IAA for 30 min to pre-establish full target inhibition or degradation. Newly synthesized RNA was labeled for indicated time spans (45 min or 60 min) at a final concentration of 100µM 4- thiouridine (4sU, Carbosynth). Adherent cells were harvested by direct snap-freezing of plates on dry ice. Suspension cells were spun down and immediately snap-frozen. RNA extraction was performed using the RNeasy Plus Mini Kit (Qiagen).

Total RNA was subjected to alkylation by iodoacetamide (Sigma, 10mM) for 15 min and RNA was repurified by ethanol precipitation. 500ng alkylated RNA were used as input for generating 3’-end mRNA sequencing libraries using a commercially available kit (QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina and PCR Add-on Kit for Illumina, Lexogen). Deep sequencing was performed using HiSeq1500 and HiSeq2500 platforms (Illumina).

0.06724463 0.04916348 0.03728357 0.05075007 0.03331248 0.0346662 0.03265504 0.04416262 0.05574821 0.05845953 0.05531433 0.06175393 0.03181749 0.02940226 0.0306263 0.04004278

In [66]:
mkdir ../results/$project
In [96]:
pd.DataFrame(tccounts.values.astype(float)/readcounts.mean().values*100, columns=tccounts.columns, index=tccounts.index).to_csv('../results/' + project + '/'+version + '_'+str(minvar_toremove)+'_'+str(mincount_toremove)+'_ratio.csv')
In [97]:
col = tccounts.columns.tolist()
col.sort()
tccounts = tccounts[col]
In [98]:
col = readcounts.columns.tolist()
col.sort()
readcounts = readcounts[col]
In [28]:
readcounts
Out[28]:
mr193-MV411-MYBi_30m-r1_tcount mr194-MV411-MYBi_30m-r2_tcount mr195-MV411-MYBi_30m-r3_tcount mr196-MV411-MYBi_30m-r4_tcount mr197-MV411-PBS_30m-r1_tcount mr198-MV411-PBS_30m-r2_tcount mr199-MV411-PBS_30m-r3_tcount mr200-MV411-PBS_30m-r4_tcount mr201-MV411-MYBi_6h-r1_tcount mr202-MV411-MYBi_6h-r2_tcount ... mr210-MV411-MS2-r3_tcount mr211-MV411-JQ1-r1_tcount mr212-MV411-JQ1-r2_tcount mr213-MV411-JQ1-r3_tcount mr214-MV411-MS2_JQ1-r1_tcount mr215-MV411-MS2_JQ1-r2_tcount mr216-MV411-MS2_JQ1-r3_tcount mr217-MV411-DMSO-r1_tcount mr218-MV411-DMSO-r2_tcount mr219-MV411-DMSO-r3_tcount
A2M 4 2 3 1 0 3 3 3 1 0 ... 2 0 2 5 2 0 0 0 0 1
NAT1 33 41 65 29 77 68 38 74 37 32 ... 182 151 105 146 134 175 165 172 170 124
AAMP 540 512 829 523 603 842 584 741 400 553 ... 1601 1827 1399 1615 1652 1476 1566 1275 1481 739
AARS1 1230 1038 2124 1022 1616 2363 1263 1719 276 352 ... 2508 1390 1157 1335 2181 2127 2355 1083 1278 671
ABAT 109 93 174 107 176 165 107 151 23 11 ... 179 123 111 146 212 207 276 136 152 116
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
107080638 281 221 502 264 408 517 274 359 138 132 ... 940 896 800 921 1123 1132 1176 815 872 647
107080644 0 0 2 0 1 1 1 1 0 0 ... 1 0 0 2 6 0 6 2 0 1
BOLA2-SMG1P6 4 8 6 6 9 6 3 7 6 4 ... 17 15 17 12 11 18 13 11 18 6
107303344 126 96 230 81 165 200 145 161 33 25 ... 111 75 72 69 109 80 149 81 84 64
SCARNA18B 1 2 6 1 2 1 1 1 5 2 ... 5 1 1 4 0 0 1 0 0 0

15731 rows × 27 columns

In [95]:
readcounts.to_csv('../results/'+project+'/'+version+'_'+str(minvar_toremove)+'_'+str(mincount_toremove)+'_readcounts.csv',index=False)
tccounts.to_csv('../results/'+project+'/'+version+'_'+str(minvar_toremove)+'_'+str(mincount_toremove)+'_tccounts.csv',index=False)
In [22]:
readcounts = pd.read_csv('../results/'+project+'/'+version+'_'+str(minvar_toremove)+'_'+str(mincount_toremove)+'_readcounts.csv')
tccounts = pd.read_csv('../results/'+project+'/'+version+'_'+str(minvar_toremove)+'_'+str(mincount_toremove)+'_tccounts.csv')

make more dataframes

In [99]:
mtccounts = pd.DataFrame()
mreadcounts = pd.DataFrame()
for i in set([i.split('-')[2] for i in tccounts.columns]):
    mtccounts[i] = tccounts[[v for v in tccounts.columns if i in v]].mean(1)
    mreadcounts[i] = readcounts[[v for v in readcounts.columns if i in v]].mean(1)
In [100]:
mtccounts.to_csv("../results/"+project+'/'+version+'_'+str(minvar_toremove)+'_'+str(mincount_toremove)+"_mean_tccounts.csv")
mreadcounts.to_csv("../results/"+project+'/'+version+'_'+str(minvar_toremove)+'_'+str(mincount_toremove)+"_mean_readcounts.csv")
In [101]:
mtccounts = pd.DataFrame()
mreadcounts = pd.DataFrame()
for i in set([i.split('-')[2] for i in tccounts.columns]):
    mtccounts[i] = tccounts[[v for v in tccounts.columns if i in v]].median(1)
    mreadcounts[i] = readcounts[[v for v in readcounts.columns if i in v]].median(1)
In [102]:
mtccounts.to_csv("../results/"+project+'/'+version+'_'+str(minvar_toremove)+'_'+str(mincount_toremove)+"_median_tccounts.csv")
mreadcounts.to_csv("../results/"+project+'/'+version+'_'+str(minvar_toremove)+'_'+str(mincount_toremove)+"_median_readcounts.csv")
In [103]:
(tccounts/readcounts).fillna(0).to_csv("../results/"+project+'/'+version+'_'+str(minvar_toremove)+'_'+str(mincount_toremove)+"_tccounts_per_readcounts.csv")

lets look at the similarity accross replicates

we have some outliers, else it seems to make some sense and on average, to be extremelly similar!

In [104]:
tccounts.columns = [i.replace('-','.') for i in tccounts.columns]
readcounts.columns = [i.replace('-','.') for i in readcounts.columns]
In [86]:
mkdir ../results/$project/plots/
In [105]:
tccounts
Out[105]:
mr252.MV411_MEF2D.DMSO_2h.r1_tcount mr253.MV411_MEF2D.DMSO_2h.r2_tcount mr254.MV411_MEF2D.DMSO_2h.r3_tcount mr255.MV411_MEF2D.DMSO_2h.r4_tcount mr256.MV411_MEF2D.VHL_2h.r1_tcount mr257.MV411_MEF2D.VHL_2h.r2_tcount mr258.MV411_MEF2D.VHL_2h.r3_tcount mr259.MV411_MEF2D.VHL_2h.r4_tcount mr260.MV411_MEF2D.DMSO_24h.r1_tcount mr261.MV411_MEF2D.DMSO_24h.r2_tcount ... mr265.MV411_MEF2D.VHL_24h.r2_tcount mr266.MV411_MEF2D.VHL_24h.r3_tcount mr267.MV411_MEF2D.VHL_24h.r4_tcount mr268.MV411.PBS_24h.r1_tcount mr269.MV411.PBS_24h.r2_tcount mr270.MV411.PBS_24h.r3_tcount mr271.MV411.PBS_24h.r4_tcount mr272.MV411.MYBi_24h.r1_tcount mr273.MV411.MYBi_24h.r2_tcount mr274.MV411.MYBi_24h.r3_tcount
A1BG 0 0 0 0 0 0 0 0 0 0 ... 0 0 0 0 0 0 0 0 0 0
NAT1 4 3 18 25 3 0 3 21 5 0 ... 3 0 0 1 0 9 0 0 0 0
AAMP 7 5 17 10 5 1 11 19 18 0 ... 15 0 1 7 0 21 0 0 0 0
AARS1 13 11 18 25 12 4 9 57 35 2 ... 10 0 2 2 0 19 1 0 0 2
ABAT 1 1 2 3 0 0 0 5 6 0 ... 5 0 0 1 0 5 0 0 0 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
107080638 0 2 1 9 1 0 3 3 5 0 ... 4 0 0 0 0 1 0 0 0 0
107080644 0 0 0 0 0 0 0 1 0 0 ... 1 0 0 0 0 0 0 0 0 0
BOLA2-SMG1P6 0 0 0 1 0 0 0 2 0 0 ... 4 0 0 0 0 0 0 0 0 0
107303344 1 0 2 1 1 0 0 1 0 0 ... 0 0 0 0 0 1 0 0 1 0
SCARNA18B 0 0 2 1 0 0 0 3 3 0 ... 0 0 0 0 0 0 0 0 4 0

16289 rows × 23 columns

In [106]:
(tccounts.loc["MYC"]/tccounts.mean(0)) /(readcounts.loc["MYC"]/readcounts.mean(0))
Out[106]:
mr252.MV411_MEF2D.DMSO_2h.r1_tcount     20.906873
mr253.MV411_MEF2D.DMSO_2h.r2_tcount     19.818364
mr254.MV411_MEF2D.DMSO_2h.r3_tcount     15.779573
mr255.MV411_MEF2D.DMSO_2h.r4_tcount     15.709042
mr256.MV411_MEF2D.VHL_2h.r1_tcount      16.630023
mr257.MV411_MEF2D.VHL_2h.r2_tcount      37.013294
mr258.MV411_MEF2D.VHL_2h.r3_tcount      22.111163
mr259.MV411_MEF2D.VHL_2h.r4_tcount      12.809547
mr260.MV411_MEF2D.DMSO_24h.r1_tcount    14.052167
mr261.MV411_MEF2D.DMSO_24h.r2_tcount    21.296080
mr262.MV411_MEF2D.DMSO_24h.r3_tcount    14.070035
mr263.MV411_MEF2D.DMSO_24h.r4_tcount    14.261005
mr264.MV411_MEF2D.VHL_24h.r1_tcount     19.960913
mr265.MV411_MEF2D.VHL_24h.r2_tcount     18.007882
mr266.MV411_MEF2D.VHL_24h.r3_tcount     37.545131
mr267.MV411_MEF2D.VHL_24h.r4_tcount     38.671184
mr268.MV411.PBS_24h.r1_tcount           15.098137
mr269.MV411.PBS_24h.r2_tcount           31.536246
mr270.MV411.PBS_24h.r3_tcount           11.012571
mr271.MV411.PBS_24h.r4_tcount           22.792705
mr272.MV411.MYBi_24h.r1_tcount          19.931377
mr273.MV411.MYBi_24h.r2_tcount           4.800348
mr274.MV411.MYBi_24h.r3_tcount           8.694439
dtype: float64
In [107]:
%matplotlib inline
sns.heatmap(tccounts.corr(), 
            xticklabels=tccounts.columns,
            yticklabels=tccounts.columns)
plt.savefig('../results/'+project+'/plots/'+version+'_similarity_replicates_sorted_readcounts.pdf')
In [108]:
%matplotlib inline
sns.heatmap(readcounts.corr(), 
            xticklabels=readcounts.columns,
            yticklabels=readcounts.columns)
plt.savefig('../results/'+project+'/plots/'+version+'_similarity_replicates.pdf')
In [110]:
%matplotlib inline
sns.heatmap(readcounts[readcounts.columns[:16]].corr(), 
            xticklabels=readcounts.columns[:16],
            yticklabels=readcounts.columns[:16])
plt.savefig('../results/'+project+'/plots/'+version+'_similarity_replicates_MYBi.pdf')

The change with DMSO (PBS) 30m vs 6h is as striking to as the change with MYBi highlighting the impact of batches

A quick detour to look for clustering

Getting the Core TF information

In [111]:
ctf=pd.read_csv('../data/CTF.csv',header=None)[0].values.tolist()
ctf
Out[111]:
['ARID2',
 'CEBPA',
 'CEBPE',
 'E2F3',
 'FLI1',
 'FOSL2',
 'GFI1',
 'GFI1B',
 'HHEX',
 'IRF8',
 'LYL1',
 'MEF2C',
 'MEF2D',
 'MEIS1',
 'MTF1',
 'MYB',
 'MYC',
 'PLAGL2',
 'RUNX1',
 'RUNX2',
 'RXRA',
 'SETDB1',
 'SNAPC5',
 'SP1',
 'SPI1',
 'SREBF1',
 'STAT5B',
 'TERF2',
 'TFAP4',
 'ZEB2',
 'ZFPM1',
 'ZMYND8',
 'LMO2',
 'MAX',
 'ELF2',
 'ETV6',
 'HOXA9',
 'GATA2']
In [112]:
set(ctf) & set(tccounts.index)
Out[112]:
{'ARID2',
 'CEBPA',
 'CEBPE',
 'E2F3',
 'ELF2',
 'ETV6',
 'FLI1',
 'FOSL2',
 'GATA2',
 'GFI1',
 'GFI1B',
 'HHEX',
 'HOXA9',
 'IRF8',
 'LMO2',
 'LYL1',
 'MAX',
 'MEF2C',
 'MEF2D',
 'MEIS1',
 'MTF1',
 'MYB',
 'MYC',
 'PLAGL2',
 'RUNX1',
 'RUNX2',
 'RXRA',
 'SETDB1',
 'SNAPC5',
 'SP1',
 'SPI1',
 'SREBF1',
 'STAT5B',
 'TERF2',
 'TFAP4',
 'ZEB2',
 'ZFPM1',
 'ZMYND8'}
In [113]:
ctfpos = [val for val in tccounts.index if val in ctf]
notctfpos = [val for val in tccounts.index if val not in ctf]
In [114]:
ctfpos.extend(['EGR1','SERTAD1'])

We find a CTF not in the dataset

Let's look at how they change accross time

how core transcription factors change accross time when the cell is with JQ1 conditions

we are looking at the difference between production of each CTF compared to the average RNA production with JQ1 and without JQ1

DESEQ ANALYSIS

In [115]:
readcounts["genes"] = readcounts.index
readcounts = readcounts.reset_index(drop=True)
tccounts["genes"] = tccounts.index
tccounts = tccounts.reset_index(drop=True)
In [223]:
tccountsMEF2D= tccounts[tccounts.columns[:16]]
designMEF2D2 = pd.DataFrame(index= [i.replace('-','.') for i in tccountsMEF2D.columns], 
                      columns=['DMSO','VHL'], 
                      data=np.array([[1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0],
                                     [0,0,0,0,1,1,1,1,0,0,0,0,0,0,0,0]],dtype=bool).T)
designMEF2D24 = pd.DataFrame(index=[i.replace('-','.') for i in tccountsMEF2D.columns], 
                      columns=['DMSO','VHL'], 
                      data=np.array([[0,0,0,0,0,0,0,0,1,1,1,1,0,0,0,0],
                                     [0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1]],dtype=bool).T)
In [123]:
tccountsMybi[tccountsMybi.columns[np.array(Mybi+[1],np.bool)]]
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-123-8f3347ffe36b> in <module>
----> 1 tccountsMybi[tccountsMybi.columns[np.array(Mybi+[1],np.bool)]]

NameError: name 'Mybi' is not defined
In [224]:
### MYCi
tccountsMybi= tccounts[tccounts.columns[16:-1]]
designMybi24 = pd.DataFrame(index=[i.replace('-','.') for i in tccountsMybi.columns], 
                      columns=['DMSO','VHL'], 
                      data=np.array([[1,1,1,1,0,0,0],
                                     [0,0,0,0,1,1,1]],dtype=bool).T)

Differential gene expression analysis, PCA and GO-term enrichment

For gene-level analysis, raw reads mapped to different UTR annotations of the same gene were summed up by Entrez Gene ID. Pilot studies of K562 cells with kinase inhibitors were performed as single experiments.

Analysis of differential gene expression was restricted to genes with ≥ 10 reads in at least one condition for 50bp sequencing runs (flavopiridol and DMSO) or ≥ 20 reads in at least one condition for 100bp sequencing runs (mk2206, trametinib, nilotinib, trametinib + mk2206 and DMSO). For estimating differential expression, a pseudo-count of 1 raw read was added to all genes.

All other SLAM-seq experiments were performed in triplicates and analyzed as follows.

Differential gene expression calling was performed on raw read counts with ≥ 2 T>C conversions using DESeq2 (version 1.14.1) with default settings, and with size factors estimated on corresponding total mRNA reads for global normalization.

Downstream analysis was restricted to genes passing all internal filters for FDR estimation by DESeq2. Principal component analysis was performed after variance stabilizing transformation on the 500 most variable genes across all conditions of a given experiment. GO-term enrichment analysis was performed on genes significantly and strongly downregulated (FDR ≤ 0.1, log2FC ≤ -1) in SLAM-seq upon IAA-treatment in K562MYC-AID + Tir1 by the PANTHER Overrepresentation Test (Fisher's Exact with FDR multiple test correction, release 20171205, http://pantherdb.org) on GO Ontology database Released 2017-12-27.

In [275]:
scaling="ERCCtrial"

Mybi

In [256]:
Mybi = [1,1,1,1,1,1,1]
tccountsMybi= tccounts[tccounts.columns[16:]]
deseqMybi = pyDESeq2.pyDESeq2(count_matrix=tccountsMybi[tccountsMybi.columns[np.array(Mybi+[1],np.bool)]], design_matrix=designMybi24[np.array(Mybi,np.bool)],
                         design_formula="~DMSO - VHL",
                         gene_column="genes")
3.3.2

MEF2D

In [257]:
MEF2D2 = [1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0]
tccountsMEF2D= tccounts[list(tccounts.columns[:16])+list(tccounts.columns[-1:])]
deseqMEF2D2 = pyDESeq2.pyDESeq2(count_matrix = tccountsMEF2D[tccountsMEF2D.columns[np.array(MEF2D2+[1],np.bool)]],
                         design_matrix=designMEF2D2[np.array(MEF2D2,np.bool)],
                         design_formula="~DMSO - VHL",
                         gene_column="genes")
MEF2D24 = [0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1]
deseqMEF2D24 = pyDESeq2.pyDESeq2(count_matrix = tccountsMEF2D[tccountsMEF2D.columns[np.array(MEF2D24+[1],np.bool)]],
                         design_matrix=designMEF2D24[np.array(MEF2D24,np.bool)],
                         design_formula="~DMSO - VHL",
                         gene_column="genes")
3.3.2
3.3.2

estimating size factors

MYCi

In [10]:
readcountsMyci= readcounts[readcounts.columns[15:-1]]

deseqMS2.run_estimate_size_factors(geoMeans = np.exp(np.mean(np.log(
    readcountsMyci[readcountsMyci.columns[np.array([1,1,1,0,0,0,0,0,0,0,0,0], np.bool)]].values+1), 1)))
In [174]:
readcountsMybi= readcounts[readcounts.columns[:15]]

deseqMybi30.run_estimate_size_factors(geoMeans = np.exp(np.mean(np.log(readcountsMybi[readcountsMybi.columns[
        np.array([1,1,1,1,0,0,0,0,0,0,0,0,0,0,0],np.bool)]].values+1),1)))
deseqMybi6.run_estimate_size_factors(geoMeans = np.exp(np.mean(np.log(readcountsMybi[readcountsMybi.columns[
        np.array([0,0,0,0,0,0,0,0,1,1,1,1,0,0,0],np.bool)]].values+1),1)))
In [276]:
readcountsMEF2D= readcounts[readcounts.columns[:16]]

deseqMEF2D2.run_estimate_size_factors(geoMeans = np.exp(np.mean(np.log(readcountsMEF2D[readcountsMEF2D.columns[
        np.array([1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0],np.bool)]].values+1),1)))
deseqMEF2D24.run_estimate_size_factors(geoMeans = np.exp(np.mean(np.log(readcountsMEF2D[readcountsMEF2D.columns[
        np.array([0,0,0,0,0,0,0,0,1,1,1,1,0,0,0,0],np.bool)]].values+1),1)))
In [277]:
readcountsMybi= readcounts[readcounts.columns[16:-1]]

deseqMybi.run_estimate_size_factors(geoMeans = np.exp(np.mean(np.log(
    readcountsMybi[readcountsMybi.columns[np.array([1,1,1,1,0,0,0], np.bool)]].values+1), 1)))

other size factor estimations

In [135]:
# from https://www.cell.com/trends/genetics/pdf/S0168-9525(13)00089-9.pdf FFROM THOUSANDS OF SAMPLES
housekeeping1 = ["C1orf43", "CHMP2A", "EMC7", "GPI", "PSMB2", "PSMB4", "RAB7A", "REEP5", "SNRPD3", "VCP", "VPS29"]

#https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4760967/ FOR CANCER CELL LINES
housekeeping2 = ['18S rRNA',
'ACTB',
'B2M',
'G6PD',
'GAPDH',
'GUSB',
'HMBS',
'HPRT1',
'PGK1',
'PPIA',
'RPL13a',
'SDHA',
'TBP',
'TUBB',
'YWHAZ']
In [136]:
housekeeping = readcounts.genes.isin(housekeeping2)
In [139]:
readcountsMybi= readcounts[readcounts.columns[16:-1]]
np.exp(np.mean(np.log(
    readcountsMybi[readcountsMybi.columns[np.array([1,1,1,1,0,0,0], np.bool)]].values+1), 1))
Out[139]:
array([  2.37841423,  65.42519431, 836.23056631, ...,   9.36138928,
        95.49529375,   1.        ])
In [231]:
readcountsMybi= readcounts[readcounts.columns[16:-1]]

deseqMybi.run_estimate_size_factors(geoMeans = np.exp(np.mean(np.log(
    readcountsMybi[readcountsMybi.columns[np.array([1,1,1,1,0,0,0], np.bool)]].values+1), 1)), controlGenes=housekeeping)
In [232]:
readcountsMEF2D= readcounts[readcounts.columns[:16]]

deseqMEF2D2.run_estimate_size_factors(geoMeans = np.exp(np.mean(np.log(readcountsMEF2D[readcountsMEF2D.columns[
        np.array([1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0],np.bool)]].values+1),1)), controlGenes=housekeeping)
deseqMEF2D24.run_estimate_size_factors(geoMeans = np.exp(np.mean(np.log(readcountsMEF2D[readcountsMEF2D.columns[
        np.array([0,0,0,0,0,0,0,0,1,1,1,1,0,0,0,0],np.bool)]].values+1),1)), controlGenes=housekeeping)

Modifying size factors

In [278]:
sizeFact = deseqMybi.getSizeFactors()
In [279]:
sizeFact
Out[279]:
array([1.72875705, 0.61936245, 7.2332409 , 0.68908538, 0.31830308,
       0.9602762 , 0.61302502])
In [207]:
r
Out[207]:
{'DMSO_2h': [0.2243153232470735, 0.02204177171648129],
 'VHL_2h': [0.23495725535742493, 0.012366178880134462],
 'DMSO_24h': [0.14047889898493598, 0.0068663572605201255],
 'VHL_24h': [0.1960673739532328, 0.04013998428238451],
 'PBS_24h': [0.23538398133738964, 0.06424715552832781],
 'MYBi_24h': [1.0041758119681277, 0.13391993501133953]}
In [280]:
sizeFact[4:] = sizeFact[4:]*(r['MYBi_24h'][0]/r['PBS_24h'][0])
In [281]:
deseqMybi.setSizeFactors(sizeFact)
In [282]:
sizeFact = deseqMEF2D24.getSizeFactors()
In [283]:
sizeFact[4:] = sizeFact[4:]*(r['VHL_24h'][0]/r['DMSO_24h'][0])
In [284]:
deseqMEF2D24.setSizeFactors(sizeFact)

running it

In [285]:
deseqMybi.run_deseq()
deseqMybi.get_deseq_result()
resMybi = deseqMybi.deseq_result
resMybi.pvalue = np.nan_to_num(np.array(resMybi.pvalue), 1)
resMybi.log2FoldChange = np.nan_to_num(np.array(resMybi.log2FoldChange), 0)
resMybi.log2FoldChange = -resMybi.log2FoldChange
resMybi["gene_id"] = resMybi.genes
R[write to console]: using pre-existing size factors

R[write to console]: estimating dispersions

R[write to console]: found already estimated dispersions, replacing these

R[write to console]: gene-wise dispersion estimates

R[write to console]: mean-dispersion relationship

R[write to console]: final dispersion estimates

R[write to console]: fitting model and testing

In [286]:
deseqMEF2D2.run_deseq()
deseqMEF2D24.run_deseq()
deseqMEF2D2.get_deseq_result()
deseqMEF2D24.get_deseq_result()
resMEF2D2 = deseqMEF2D2.deseq_result
resMEF2D24 = deseqMEF2D24.deseq_result
resMEF2D2.pvalue = np.nan_to_num(np.array(resMEF2D2.pvalue), 1)
resMEF2D2.log2FoldChange = np.nan_to_num(np.array(resMEF2D2.log2FoldChange), 0)
resMEF2D24.pvalue = np.nan_to_num(np.array(resMEF2D24.pvalue), 1)
resMEF2D24.log2FoldChange = np.nan_to_num(np.array(resMEF2D24.log2FoldChange), 0)
resMEF2D24.log2FoldChange = -resMEF2D24.log2FoldChange
resMEF2D2.log2FoldChange = -resMEF2D2.log2FoldChange
resMEF2D2["gene_id"] = resMEF2D2.genes
resMEF2D24["gene_id"] = resMEF2D24.genes
R[write to console]: using pre-existing size factors

R[write to console]: estimating dispersions

R[write to console]: found already estimated dispersions, replacing these

R[write to console]: gene-wise dispersion estimates

R[write to console]: mean-dispersion relationship

R[write to console]: final dispersion estimates

R[write to console]: fitting model and testing

R[write to console]: using pre-existing size factors

R[write to console]: estimating dispersions

R[write to console]: found already estimated dispersions, replacing these

R[write to console]: gene-wise dispersion estimates

R[write to console]: mean-dispersion relationship

R[write to console]: final dispersion estimates

R[write to console]: fitting model and testing

In [92]:
deseqMS2.run_deseq()
deseqJQ1.run_deseq()
deseqMS2_JQ1.run_deseq()
deseqMS2.get_deseq_result()
deseqJQ1.get_deseq_result()
deseqMS2_JQ1.get_deseq_result()
resMS2 = deseqMS2.deseq_result
resJQ1 = deseqJQ1.deseq_result
resMS2_JQ1 = deseqMS2_JQ1.deseq_result
resMS2.pvalue = np.nan_to_num(np.array(resMS2.pvalue), 1)
resMS2.log2FoldChange = np.nan_to_num(np.array(resMS2.log2FoldChange), 0)
resJQ1.pvalue = np.nan_to_num(np.array(resJQ1.pvalue), 1)
resJQ1.log2FoldChange = np.nan_to_num(np.array(resJQ1.log2FoldChange), 0)
resMS2_JQ1.pvalue = np.nan_to_num(np.array(resMS2_JQ1.pvalue), 1)
resMS2_JQ1.log2FoldChange = np.nan_to_num(np.array(resMS2_JQ1.log2FoldChange), 0)
resMS2.log2FoldChange = -resMS2.log2FoldChange
resJQ1.log2FoldChange = -resJQ1.log2FoldChange
resMS2_JQ1.log2FoldChange = -resMS2_JQ1.log2FoldChange
resMS2["gene_id"] = resMS2.genes
resJQ1["gene_id"] = resJQ1.genes
resMS2_JQ1["gene_id"] = resMS2_JQ1.genes
R[write to console]: using pre-existing size factors

R[write to console]: estimating dispersions

R[write to console]: found already estimated dispersions, replacing these

R[write to console]: gene-wise dispersion estimates

R[write to console]: mean-dispersion relationship

R[write to console]: final dispersion estimates

R[write to console]: fitting model and testing

R[write to console]: using pre-existing size factors

R[write to console]: estimating dispersions

R[write to console]: found already estimated dispersions, replacing these

R[write to console]: gene-wise dispersion estimates

R[write to console]: mean-dispersion relationship

R[write to console]: final dispersion estimates

R[write to console]: fitting model and testing

R[write to console]: using pre-existing size factors

R[write to console]: estimating dispersions

R[write to console]: found already estimated dispersions, replacing these

R[write to console]: gene-wise dispersion estimates

R[write to console]: mean-dispersion relationship

R[write to console]: final dispersion estimates

R[write to console]: fitting model and testing

In [468]:
deseqMybi30.run_deseq()
deseqMybi6.run_deseq()
deseqMybi30.get_deseq_result()
deseqMybi6.get_deseq_result()
resMybi30 = deseqMybi30.deseq_result
resMybi6 = deseqMybi6.deseq_result
resMybi30.pvalue = np.nan_to_num(np.array(resMybi30.pvalue), 1)
resMybi30.log2FoldChange = np.nan_to_num(np.array(resMybi30.log2FoldChange), 0)
resMybi6.pvalue = np.nan_to_num(np.array(resMybi6.pvalue), 1)
resMybi6.log2FoldChange = np.nan_to_num(np.array(resMybi6.log2FoldChange), 0)
resMybi6.log2FoldChange = -resMybi6.log2FoldChange
resMybi30.log2FoldChange = -resMybi30.log2FoldChange
resMybi30["gene_id"] = resMybi30.genes
resMybi6["gene_id"] = resMybi6.genes
R[write to console]: using pre-existing size factors

R[write to console]: estimating dispersions

R[write to console]: found already estimated dispersions, replacing these

R[write to console]: gene-wise dispersion estimates

R[write to console]: mean-dispersion relationship

R[write to console]: final dispersion estimates

R[write to console]: fitting model and testing

R[write to console]: using pre-existing size factors

R[write to console]: estimating dispersions

R[write to console]: found already estimated dispersions, replacing these

R[write to console]: gene-wise dispersion estimates

R[write to console]: mean-dispersion relationship

R[write to console]: -- note: fitType='parametric', but the dispersion trend was not well captured by the
   function: y = a/x + b, and a local regression fit was automatically substituted.
   specify fitType='local' or 'mean' to avoid this message next time.

R[write to console]: final dispersion estimates

R[write to console]: fitting model and testing

PLOTS

whisker's plots

In [141]:
%matplotlib inline
In [469]:
res = resMybi30[resMybi30.baseMean>10]
res.baseMean= np.log2(1+res.baseMean)
res["type"] = ['ctf' if i else "other" for i in  res.genes.isin(ctf)]
/home/jeremie/.local/lib/python3.8/site-packages/pandas/core/generic.py:5303: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  self[name] = value
<ipython-input-469-48ffebc3b001>:3: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  res["type"] = ['ctf' if i else "other" for i in  res.genes.isin(ctf)]
In [470]:
ax = sns.boxplot(data=res,x='type',y='log2FoldChange').set_title("Mybi at 30mn foldChange")
ax.figure.savefig('../results/'+project+"/plots/"+version+"_"+scaling+"_whiskersMybi_30mn_logfch.pdf")
In [471]:
ax =sns.boxplot(data=res,x='type',y='baseMean')
ax.set_title("Mybi 30mn baseMean")
ax.figure.savefig('../results/'+project+"/plots/"+version+"_"+scaling+"_whiskers_Mybi_30mn_baseMean.pdf")
In [205]:
res = resMybi6[resMybi6.baseMean>10]
res.baseMean= np.log2(1+res.baseMean)
res["type"] = ['ctf' if i else "other" for i in  res.genes.isin(ctf)]
/home/jeremie/.local/lib/python3.8/site-packages/pandas/core/generic.py:5303: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  self[name] = value
<ipython-input-205-82478fb37811>:3: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  res["type"] = ['ctf' if i else "other" for i in  res.genes.isin(ctf)]
In [206]:
ax= sns.boxplot(data=res,x='type',y='log2FoldChange')
ax.set_title("Mybi at 6h foldchange")
ax.figure.savefig('../results/'+project+"/plots/"+version+"_"+scaling+"_whiskers_Mybi_6h_logfch.pdf")
In [207]:
ax = sns.boxplot(data=res,x='type',y='baseMean')
ax.set_title("Mybi at 6h baseMean")
ax.figure.savefig('../results/'+project+"/plots/"+version+"_"+scaling+"_whiskers_Mybi_6h_baseMean.pdf")
In [287]:
res = resMybi[resMybi.baseMean>10]
res.baseMean= np.log2(1+res.baseMean)
res["type"] = ['ctf' if i else "other" for i in  res.genes.isin(ctf)]
/home/jeremie/.local/lib/python3.8/site-packages/pandas/core/generic.py:5303: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  self[name] = value
<ipython-input-287-9c3423f32532>:3: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  res["type"] = ['ctf' if i else "other" for i in  res.genes.isin(ctf)]
In [288]:
ax= sns.boxplot(data=res,x='type',y='log2FoldChange')
ax.set_title("Mybi at 24h foldchange")
ax.figure.savefig('../results/'+project+"/plots/"+version+"_"+scaling+"_whiskers_Mybi_24h_logfch.pdf")
In [289]:
ax = sns.boxplot(data=res,x='type',y='baseMean')
ax.set_title("Mybi at 24h baseMean")
ax.figure.savefig('../results/'+project+"/plots/"+version+"_"+scaling+"_whiskers_Mybi_24h_baseMean.pdf")

MEF2D

In [290]:
res = resMEF2D2[resMEF2D2.baseMean>10]
res.baseMean= np.log2(1+res.baseMean)
res["type"] = ['ctf' if i else "other" for i in  res.genes.isin(ctf)]
/home/jeremie/.local/lib/python3.8/site-packages/pandas/core/generic.py:5303: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  self[name] = value
<ipython-input-290-7dea2ee8b938>:3: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  res["type"] = ['ctf' if i else "other" for i in  res.genes.isin(ctf)]
In [291]:
ax= sns.boxplot(data=res,x='type',y='log2FoldChange')
ax.set_title("MEF2D at 2h foldchange")
ax.figure.savefig('../results/'+project+"/plots/"+version+"_"+scaling+"_whiskers_MEF2D_2h_logfch.pdf")
In [292]:
ax = sns.boxplot(data=res,x='type',y='baseMean')
ax.set_title("MEF2D at 2h baseMean")
ax.figure.savefig('../results/'+project+"/plots/"+version+"_"+scaling+"_whiskers_MEF2D_2h_baseMean.pdf")
In [293]:
res = resMEF2D24[resMEF2D24.baseMean>10]
res.baseMean= np.log2(1+res.baseMean)
res["type"] = ['ctf' if i else "other" for i in  res.genes.isin(ctf)]
/home/jeremie/.local/lib/python3.8/site-packages/pandas/core/generic.py:5303: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  self[name] = value
<ipython-input-293-bc2ba62415de>:3: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  res["type"] = ['ctf' if i else "other" for i in  res.genes.isin(ctf)]
In [294]:
ax= sns.boxplot(data=res,x='type',y='log2FoldChange')
ax.set_title("MEF2D at 24h foldchange")
ax.figure.savefig('../results/'+project+"/plots/"+version+"_"+scaling+"_whiskers_MEF2D_24h_logfch.pdf")
In [295]:
ax = sns.boxplot(data=res,x='type',y='baseMean')
ax.set_title("MEF2D at 24h baseMean")
ax.figure.savefig('../results/'+project+"/plots/"+version+"_"+scaling+"_whiskers_MEF2D_24h_baseMean.pdf")
Myci
In [96]:
res = resJQ1[resJQ1.baseMean>10]
res.baseMean= np.log2(1+res.baseMean)
res["type"] = ['ctf' if i else "other" for i in  res.genes.isin(ctf)]
/home/jeremie/.local/lib/python3.8/site-packages/pandas/core/generic.py:5303: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  self[name] = value
<ipython-input-96-625ed54343ef>:3: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  res["type"] = ['ctf' if i else "other" for i in  res.genes.isin(ctf)]
In [97]:
ax = sns.boxplot(data=res,x='type',y='log2FoldChange')
ax.set_title("JQ1 foldchange")
ax.figure.savefig('../results/'+project+"/plots/"+version+"_"+scaling+"_whiskers_JQ1_logfch.pdf")
In [98]:
ax =sns.boxplot(data=res,x='type',y='baseMean')
ax.set_title("JQ1 base")
ax.figure.savefig('../results/'+project+"/plots/"+version+"_"+scaling+"_whiskers_JQ1_baseMean.pdf")
In [99]:
res = resMS2[resMS2.baseMean>10]
res.baseMean= np.log2(1+res.baseMean)
res["type"] = ['ctf' if i else "other" for i in  res.genes.isin(ctf)]
/home/jeremie/.local/lib/python3.8/site-packages/pandas/core/generic.py:5303: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  self[name] = value
<ipython-input-99-e69356b5065c>:3: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  res["type"] = ['ctf' if i else "other" for i in  res.genes.isin(ctf)]
In [100]:
ax =sns.boxplot(data=res,x='type',y='log2FoldChange')
ax.set_title("MS2 foldChange")
ax.figure.savefig('../results/'+project+"/plots/"+version+"_"+scaling+"_whiskers_MS2_logfch.pdf")
In [101]:
ax = sns.boxplot(data=res,x='type',y='baseMean')
ax.set_title("MS2 Base")
ax.figure.savefig('../results/'+project+"/plots/"+version+"_"+scaling+"_whiskers_MS2_baseMean.pdf")
In [102]:
res = resMS2_JQ1[resMS2_JQ1.baseMean>10]
res.baseMean= np.log2(1+res.baseMean)
res["type"] = ['ctf' if i else "other" for i in  res.genes.isin(ctf)]
/home/jeremie/.local/lib/python3.8/site-packages/pandas/core/generic.py:5303: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  self[name] = value
<ipython-input-102-3a7f333fb32e>:3: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  res["type"] = ['ctf' if i else "other" for i in  res.genes.isin(ctf)]
In [103]:
ax = sns.boxplot(data=res,x='type',y='log2FoldChange')
ax.set_title("MS2+JQ1 foldChange")
ax.figure.savefig('../results/'+project+"/plots/"+version+"_"+scaling+"_whiskers_MS2_JQ1_logfch.pdf")
In [104]:
ax = sns.boxplot(data=res,x='type',y='baseMean')
ax.set_title("MS2+JQ1 Base")
ax.figure.savefig('../results/'+project+"/plots/"+version+"_"+scaling+"_whiskers_MS2_JQ1_baseMean.pdf")

Scatter plot comparison

In [466]:
mix = pd.DataFrame()
mix["gene_id"] = resMybi30["gene_id"]
mix['Mybi 30mn'] = resMybi30.log2FoldChange
mix['Mybi 6h'] = resMybi6.log2FoldChange
In [467]:
scatter(mix[['Mybi 30mn','Mybi 6h']].values[:12000], 
               mix['gene_id'].values.tolist()[:12000], radi= 0.06, alpha=0.3,
              colors = [0 if i in ctf else 1 for i in mix['gene_id'].values.tolist()[:12000]],
       xname="Mybi 30mn",
    yname="Mybi 6h",
       folder='../results/'+project+"/plots/"+version+"_"+scaling+"_",
       title='Mybi 30mn vs 6h differences in logFoldChange')
Out[467]:
Figure(
id = '9940', …)

Regular volcanos

In [12]:
resMS2.to_csv("../results/"+project+"/"+version+'_'+scaling+"_"+str(minvar_toremove)+'_'+str(mincount_toremove)+'_MS2_deseq.csv')
resJQ1.to_csv("../results/"+project+"/"+version+'_'+scaling+"_"+str(minvar_toremove)+'_'+str(mincount_toremove)+'_JQ1_deseq.csv')
resMS2_JQ1.to_csv("../results/"+project+"/"+version+'_'+scaling+"_"+str(minvar_toremove)+'_'+str(mincount_toremove)+'_MS2_JQ1_deseq.csv')
In [226]:
resMybi30.to_csv("../results/"+project+"/"+version+'_'+scaling+'_'+str(minvar_toremove)+'_'+str(mincount_toremove)+'_Mybi_30um_deseq.csv')
resMybi6.to_csv("../results/"+project+"/"+version+'_'+scaling+'_'+str(minvar_toremove)+'_'+str(mincount_toremove)+'_Mybi_6h_deseq.csv')
In [296]:
resMybi.to_csv("../results/"+project+"/"+version+'_'+scaling+'_'+str(minvar_toremove)+'_'+str(mincount_toremove)+'_Mybi_24h_deseq.csv')
In [297]:
resMEF2D2.to_csv("../results/"+project+"/"+version+'_'+scaling+'_'+str(minvar_toremove)+'_'+str(mincount_toremove)+'_MEF2D_2h_deseq.csv')
resMEF2D24.to_csv("../results/"+project+"/"+version+'_'+scaling+'_'+str(minvar_toremove)+'_'+str(mincount_toremove)+'_MEF2D_24h_deseq.csv')

we can conclude that we get similar results to the slamseq myc paper although it seems that our values are a bit skewed toward higher expression than what is on the slamseq paper. It mightt be explained by the pseudo count of 1 that I did not set. Because I think it would highly bias the DESeq algorithm.

In [95]:
show(volcano(resMS2,tohighlight=ctf, searchbox=True, title='DESeq results of MV411 under MS2 in volcano plot', folder='../results/'+project+'/plots/'+version+'_'+scaling+"_"+str(minvar_toremove)+'_'+str(mincount_toremove)))
show(volcano(resJQ1,tohighlight=ctf, searchbox=True, title='DESeq results of MV411 under JQ1 in volcano plot', folder='../results/'+project+'/plots/'+version+'_'+scaling+"_"+str(minvar_toremove)+'_'+str(mincount_toremove)))
show(volcano(resMS2_JQ1,tohighlight=ctf, searchbox=True, title='DESeq results of MV411 under MS2 and JQ1 in volcano plot', folder='../results/'+project+'/plots/'+version+'_'+scaling+"_"+str(minvar_toremove)+'_'+str(mincount_toremove)))

Mybi

In [112]:
resMybi30[resMybi30.gene_id=="MYB"]
Out[112]:
baseMean log2FoldChange lfcSE stat pvalue padj genes gene_id
1990 58.642225 -0.630119 0.221291 2.847465 0.004407 0.034086 MYB MYB
In [109]:
show(volcano(resMybi30,tohighlight=ctf, searchbox=True, title="Mybi at 30mn", folder='../results/'+project+'/plots/'+version+'_'+scaling+"_"+str(minvar_toremove)+'_'+str(mincount_toremove)))
In [111]:
resMybi6[resMybi6.gene_id=='MYB']
Out[111]:
baseMean log2FoldChange lfcSE stat pvalue padj genes gene_id
1990 44.896318 -0.576164 0.277444 2.07669 0.03783 0.115454 MYB MYB
In [110]:
show(volcano(resMybi6,tohighlight=ctf, searchbox=True, title="Mybi at 6h", folder='../results/'+project+'/plots/'+version+'_'+scaling+"_"+str(minvar_toremove)+'_'+str(mincount_toremove),maxvalue=50))
In [298]:
show(volcano(resMybi,tohighlight=ctf, searchbox=True, title="Mybi at 24h", folder='../results/'+project+'/plots/'+version+'_'+scaling+"_"+str(minvar_toremove)+'_'+str(mincount_toremove),maxvalue=50))

MEF2D

In [299]:
show(volcano(resMEF2D2,tohighlight=ctf, searchbox=True, title="MEF2D at 2h", folder='../results/'+project+'/plots/'+version+'_'+scaling+"_"+str(minvar_toremove)+'_'+str(mincount_toremove),maxvalue=50))
show(volcano(resMEF2D24,tohighlight=ctf, searchbox=True, title="MEF2D at 24h", folder='../results/'+project+'/plots/'+version+'_'+scaling+"_"+str(minvar_toremove)+'_'+str(mincount_toremove),maxvalue=50))
In [ ]:
 
In [ ]: